Query 002930
Match_columns 864
No_of_seqs 182 out of 247
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 13:37:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002930.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002930hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1104 Nuclear cap-binding co 100.0 4E-169 8E-174 1434.6 61.7 715 3-860 30-758 (759)
2 PF09088 MIF4G_like: MIF4G lik 100.0 2.6E-62 5.6E-67 493.2 12.9 165 306-470 2-191 (191)
3 PF09090 MIF4G_like_2: MIF4G l 100.0 5.1E-47 1.1E-51 404.7 22.3 243 486-827 1-253 (253)
4 smart00543 MIF4G Middle domain 99.6 2.6E-14 5.7E-19 145.8 15.6 171 4-192 4-178 (200)
5 KOG2140 Uncharacterized conser 99.4 2E-11 4.2E-16 136.9 25.3 384 41-488 194-625 (739)
6 PF02854 MIF4G: MIF4G domain; 99.4 6.9E-12 1.5E-16 127.9 14.9 173 4-192 4-187 (209)
7 KOG2141 Protein involved in hi 94.4 4.6 9.9E-05 49.1 21.2 130 47-192 363-498 (822)
8 KOG2051 Nonsense-mediated mRNA 93.9 0.16 3.6E-06 63.0 8.5 127 42-184 459-590 (1128)
9 smart00544 MA3 Domain in DAP-5 78.1 18 0.0004 33.6 9.7 87 328-418 16-105 (113)
10 KOG1760 Molecular chaperone Pr 71.5 38 0.00082 32.8 9.7 95 636-744 22-123 (131)
11 KOG2051 Nonsense-mediated mRNA 67.9 1.5E+02 0.0032 38.3 16.3 145 44-192 662-816 (1128)
12 PF07889 DUF1664: Protein of u 67.1 61 0.0013 31.7 10.4 26 635-660 41-66 (126)
13 PRK11637 AmiB activator; Provi 65.9 2.2E+02 0.0047 33.3 16.8 33 709-741 103-135 (428)
14 COG4372 Uncharacterized protei 65.5 46 0.001 38.1 10.3 38 644-681 74-111 (499)
15 PF02847 MA3: MA3 domain; Int 64.5 30 0.00065 32.1 7.7 100 317-420 3-107 (113)
16 PF05546 She9_MDM33: She9 / Md 58.9 1.6E+02 0.0034 31.3 12.3 39 637-675 32-70 (207)
17 PF03962 Mnd1: Mnd1 family; I 57.9 60 0.0013 33.8 9.2 38 627-664 52-89 (188)
18 PF04728 LPP: Lipoprotein leuc 57.6 55 0.0012 27.5 7.0 43 634-676 7-49 (56)
19 PRK10884 SH3 domain-containing 57.4 95 0.0021 32.9 10.6 28 642-669 91-118 (206)
20 KOG2297 Predicted translation 52.6 46 0.001 37.2 7.5 114 504-617 259-382 (412)
21 KOG1003 Actin filament-coating 51.9 2.4E+02 0.0052 29.7 12.0 108 642-758 51-160 (205)
22 KOG0994 Extracellular matrix g 51.3 5E+02 0.011 34.3 16.6 163 503-676 1417-1588(1758)
23 COG1579 Zn-ribbon protein, pos 48.8 1.5E+02 0.0032 32.2 10.5 27 636-662 51-77 (239)
24 PF10186 Atg14: UV radiation r 48.2 2.5E+02 0.0054 30.5 12.7 30 633-662 59-88 (302)
25 PF12325 TMF_TATA_bd: TATA ele 47.5 2.3E+02 0.0051 27.5 10.7 37 638-674 17-53 (120)
26 COG1579 Zn-ribbon protein, pos 47.0 1.9E+02 0.0041 31.5 11.0 51 631-681 32-82 (239)
27 PRK09039 hypothetical protein; 43.7 2.6E+02 0.0057 31.8 12.2 32 636-667 129-160 (343)
28 cd07600 BAR_Gvp36 The Bin/Amph 42.9 1.6E+02 0.0034 32.1 9.7 36 713-754 196-231 (242)
29 smart00515 eIF5C Domain at the 42.5 44 0.00095 29.7 4.7 53 564-616 2-57 (83)
30 KOG0971 Microtubule-associated 42.2 1.5E+02 0.0032 37.7 10.2 77 640-732 272-348 (1243)
31 PF12718 Tropomyosin_1: Tropom 41.2 3.7E+02 0.0081 26.7 12.4 49 633-681 17-65 (143)
32 PF10168 Nup88: Nuclear pore c 41.0 7.1E+02 0.015 31.4 16.3 38 714-752 591-628 (717)
33 PF02847 MA3: MA3 domain; Int 39.9 79 0.0017 29.2 6.2 81 38-118 29-112 (113)
34 smart00544 MA3 Domain in DAP-5 38.6 87 0.0019 29.1 6.3 80 39-118 30-112 (113)
35 COG4238 Murein lipoprotein [Ce 37.0 1.1E+02 0.0024 27.2 6.0 41 634-674 29-69 (78)
36 PF01920 Prefoldin_2: Prefoldi 36.3 86 0.0019 28.6 5.8 25 638-662 6-30 (106)
37 KOG4403 Cell surface glycoprot 33.2 77 0.0017 36.8 5.6 26 712-737 255-280 (575)
38 PF14662 CCDC155: Coiled-coil 33.1 5E+02 0.011 27.3 11.0 44 635-678 27-73 (193)
39 PRK09973 putative outer membra 33.1 1.7E+02 0.0036 26.8 6.7 40 635-674 29-68 (85)
40 TIGR02338 gimC_beta prefoldin, 32.5 4.3E+02 0.0093 24.8 11.2 37 699-735 71-107 (110)
41 PF15188 CCDC-167: Coiled-coil 31.6 3.9E+02 0.0084 24.5 8.8 38 709-746 43-81 (85)
42 PRK12472 hypothetical protein; 31.2 4E+02 0.0087 31.8 11.1 31 651-681 218-248 (508)
43 KOG2141 Protein involved in hi 30.8 1.5E+02 0.0033 36.8 7.8 70 44-114 652-721 (822)
44 TIGR03752 conj_TIGR03752 integ 30.1 3.9E+02 0.0084 31.8 10.8 26 636-661 58-83 (472)
45 PRK15396 murein lipoprotein; P 29.7 2.1E+02 0.0046 25.7 6.8 40 635-674 30-69 (78)
46 PF12061 DUF3542: Protein of u 28.9 75 0.0016 35.8 4.6 113 60-197 20-148 (402)
47 PRK11637 AmiB activator; Provi 28.8 3.9E+02 0.0085 31.2 10.9 21 713-733 100-120 (428)
48 PF05529 Bap31: B-cell recepto 28.8 3.6E+02 0.0079 27.7 9.5 16 644-659 118-133 (192)
49 cd07617 BAR_Endophilin_B2 The 28.4 4.8E+02 0.01 28.0 10.4 47 635-681 124-170 (220)
50 PF02020 W2: eIF4-gamma/eIF5/e 28.1 96 0.0021 27.7 4.5 45 574-618 2-49 (84)
51 PF07064 RIC1: RIC1; InterPro 27.7 1.8E+02 0.004 31.8 7.4 68 48-116 184-253 (258)
52 PF11570 E2R135: Coiled-coil r 27.6 4.2E+02 0.0091 26.1 8.8 41 641-681 12-52 (136)
53 PF12777 MT: Microtubule-bindi 27.2 2.1E+02 0.0046 32.5 8.1 85 630-730 200-284 (344)
54 PF00261 Tropomyosin: Tropomyo 26.3 5.3E+02 0.012 27.6 10.6 32 702-733 190-221 (237)
55 KOG3647 Predicted coiled-coil 26.3 7.2E+02 0.016 27.5 11.1 29 632-660 107-135 (338)
56 PF10234 Cluap1: Clusterin-ass 26.1 6.6E+02 0.014 27.8 11.1 45 631-675 163-207 (267)
57 cd04378 RhoGAP_GMIP_PARG1 RhoG 25.6 41 0.00088 35.2 1.8 35 375-411 5-39 (203)
58 PF08614 ATG16: Autophagy prot 24.9 3.1E+02 0.0067 28.5 8.2 38 705-742 147-184 (194)
59 COG1422 Predicted membrane pro 24.9 2.3E+02 0.0051 29.9 7.1 24 718-741 100-123 (201)
60 PF12761 End3: Actin cytoskele 24.4 1.9E+02 0.004 30.5 6.3 26 709-734 167-192 (195)
61 KOG0977 Nuclear envelope prote 23.4 1.4E+03 0.031 27.9 16.3 169 551-751 43-213 (546)
62 KOG2391 Vacuolar sorting prote 23.3 4.7E+02 0.01 29.9 9.4 16 177-192 22-37 (365)
63 PF10455 BAR_2: Bin/amphiphysi 23.0 4.8E+02 0.01 29.2 9.5 25 545-569 115-140 (289)
64 KOG0995 Centromere-associated 22.8 1.3E+03 0.028 28.3 13.3 34 806-840 413-446 (581)
65 PF08146 BP28CT: BP28CT (NUC21 22.7 92 0.002 31.3 3.6 79 345-423 36-120 (153)
66 cd07627 BAR_Vps5p The Bin/Amph 22.0 9.4E+02 0.02 25.3 16.8 48 629-676 114-168 (216)
67 PRK10698 phage shock protein P 21.9 8.5E+02 0.018 26.0 10.9 35 630-664 106-140 (222)
68 PF15290 Syntaphilin: Golgi-lo 21.4 7.5E+02 0.016 27.6 10.2 23 706-728 121-143 (305)
69 cd07592 BAR_Endophilin_A The B 21.3 8.2E+02 0.018 26.2 10.6 25 546-572 79-103 (223)
70 TIGR02977 phageshock_pspA phag 21.1 9.9E+02 0.021 25.2 11.3 33 630-662 106-138 (219)
71 PF12128 DUF3584: Protein of u 20.9 2.1E+03 0.046 29.0 17.1 35 820-854 741-775 (1201)
72 PF06632 XRCC4: DNA double-str 20.8 7E+02 0.015 28.6 10.5 13 646-658 139-151 (342)
73 KOG3595 Dyneins, heavy chain [ 20.5 2.2E+03 0.047 29.5 16.6 69 533-601 831-905 (1395)
74 PF03904 DUF334: Domain of unk 20.3 1E+03 0.022 25.8 10.7 34 714-747 125-158 (230)
No 1
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=100.00 E-value=3.5e-169 Score=1434.65 Aligned_cols=715 Identities=35% Similarity=0.628 Sum_probs=656.8
Q ss_pred cchhhHhhhccCCCCCCCCCchHhhHHHHHHHHHhhhccccCcHHHHHHHHHHhCCCCchHHHHHHHHHhcCChhHHHHH
Q 002930 3 SWKNLLLKIGDNCPEYGNSDDLKDHIETCFGVIRRELEHSSDDVPHYIINCAEQIPHKIPLYGTLVGLLNLENEDFVKKV 82 (864)
Q Consensus 3 ~~~~li~riGek~~~~~~~ss~e~~ie~La~~l~~el~~~~~~il~~l~~cv~e~P~K~p~YAtLVgllN~kn~~~g~~i 82 (864)
+.+++|.++||++ .+++|+||++|+++|.+|++++++.|++++.+||.++|+|+|+|||||||+|+||++||+++
T Consensus 30 rl~~~i~~vg~~s-----~ss~e~~l~~l~~~l~~~~~~~~~~iL~~L~~ca~~lP~K~~~yaTLvgllN~kn~~fg~~~ 104 (759)
T KOG1104|consen 30 RLESLIREVGEPS-----GSSVEDNLENLVAVLEADLENFKSKILDILNTCAVYLPEKITAYATLVGLLNLKNFNFGGEF 104 (759)
T ss_pred HHHHHHHhhcCCC-----CCcHHHhHHHHHHHHHhhHHHHHHHHHHHHHHHHHHcccchhHHHHHHHHHhccchhhHHHH
Confidence 5678899999996 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCchhHHHHHHHHhhcccccccCcccHHHHHHHHHHhhhhcccccCCCChhhhhhhHHHHHHHhhh
Q 002930 83 VETTQRKFQDALDSGNCDRIRILMRFLTVMMCSKILQPGSLVVVFETLLSSAATTVDEDKGNPSWQARADFYVTCILSCL 162 (864)
Q Consensus 83 ve~~~~~lq~~L~~g~w~~~klllRFLa~Lvn~~Vi~~~sl~~ll~~Ll~~a~~~~~~e~~~~~~q~r~D~~v~~vL~~L 162 (864)
|+++++++|+++++|+|++||.++|||++|+||+|+++++++++|++|++.|. +...| |+|+|||+||||++|
T Consensus 105 v~~~~~~~q~sl~~~~~n~ar~llrfL~dL~~~~vl~~~sli~l~esl~~~~~-----e~~~P--qvr~D~~v~~vLs~l 177 (759)
T KOG1104|consen 105 VEYMIEELQESLKSGNWNEARYLLRFLSDLSNCHVLQADSLINLFESLLDAAI-----EENVP--QVRRDYYVYCVLSSL 177 (759)
T ss_pred HHHHHHHHHHHhhcCChHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHH-----hhcCc--chhhhHHHHHHHhcc
Confidence 99999999999999999999999999999999999999999999999999874 33344 999999999999999
Q ss_pred hhccHHhhhhCHHHHHHHHHHHHHHHhhcccCCCCCcccccCCCCCCCCcchHhHHHHHHHHHHHHHhCCCcccCCCCCc
Q 002930 163 PWGGAELIEQVPEEIERVMAGLEAYLSIRRHTSDTGLSFFEEDDESGKGLVEKDFLEDLWHRVQALSSNGWKLDSVPRPH 242 (864)
Q Consensus 163 P~~G~eL~e~~~e~Le~ll~~ie~y~~~R~~~~~~ll~~~~~~~~~~~~~~~~~~L~~Lw~ql~~L~~~~W~~~~ipRpy 242 (864)
||+|++|+++.++++|+|+.+|+.|+++|+++|.++|++|+. +.+++++|||++||+||++|++|+|++++|||||
T Consensus 178 Pw~g~el~e~~~~~~e~ll~~ie~Yl~~R~~shi~lL~vw~~----~~~~~qeeyle~L~~qI~~lr~n~w~e~hIprPy 253 (759)
T KOG1104|consen 178 PWFGRELNEKKPTEMEELLVYIEIYLKKRKKSHINLLNVWSG----EPDHPQEEYLELLWAQIQKLRQNDWAENHIPRPY 253 (759)
T ss_pred chhhhhhcccchHHHHHHHHHHHHHHHHhcccccchhhcCCC----CCCchHHHHHHHHHHHHHHHHhcCcccccCCCch
Confidence 999999999999999999999999999999999999999985 3678999999999999999999999999999999
Q ss_pred chhhhhhccCCCcCCCCCCCCCCCCCCCCCCCcccCCccccccccCCccccccccccCCCC-C-----CCCCchhHHHHH
Q 002930 243 LSFEAQLVSGKSHEFGPISCPEQPDVPTAVSGITHGKQKHDAELKYPQRIRRLNIFPASKS-E-----VDMQPIDRFILE 316 (864)
Q Consensus 243 ~~f~~~L~~~~~H~lp~i~~P~~~~~~~~~~~~~~~~~~~~~~~~yP~~~~~frlf~~~~~-~-----~~~~~ier~lie 316 (864)
++|+++|+++.+|+||+++.| +|+....||.|.++||+|.++++ + .+.++|+||++|
T Consensus 254 ~~Fes~L~~~~~h~Lp~~~~p-----------------ph~~~~~yp~p~v~fR~f~~~~~~~e~p~mp~~ssi~rflfe 316 (759)
T KOG1104|consen 254 LGFESTLVHALQHNLPSFVSP-----------------PHTEDSEYPMPRVVFRMFQYTDCGFEIPTMPGASSIERFLFE 316 (759)
T ss_pred hhHHHHHHHhcccCCCCCCCC-----------------CCcccccCCcchhhhhcccccccCCCCCCCCCchhHHHHHHH
Confidence 999999999999999999977 47778889999999999999988 2 267899999999
Q ss_pred HHHHHHHHhccccHHHHHHHhhcCCCCCC---chhhHHHHHHHHhhcCCCCCCcchhHHHHHHHHHhcCCCCchHHHHHH
Q 002930 317 EYLLDVLLFFNGCRKECAFYMVNLPVPFR---YEYLMAETIFSQLLLLPQPPFKPIYYTLVIMDLCKALPGAFPAVVAGA 393 (864)
Q Consensus 317 e~i~Dii~~f~~nRKecA~~Ll~lp~t~k---~E~~iVEtIfs~lf~LP~p~~~~vYY~slLiELCK~~P~~iapvlgrA 393 (864)
++|+|||.++++|||+||++|+++|.++| +||+|||||||+||+||+|+++.+||||||+||||++|+++|||||||
T Consensus 317 ~~i~dii~sl~fnRKecA~~l~~l~~~f~~~p~eylivEtIfgell~LP~~~~~~iyy~slLiElCK~~P~~lpqV~aqa 396 (759)
T KOG1104|consen 317 EIILDIIESLEFNRKECARQLLSLPVKFKAIPIEYLIVETIFGELLRLPTPPYKTIYYTSLLIELCKLQPKALPQVLAQA 396 (759)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHcCcccccCccHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHhCccchhHHHHHH
Confidence 99999999999999999999999997655 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCcHHHHHHHHHHHHhhhcccCccccccccccccCCCCCCchHHHHHHHHHHHHhhchhHHHHHhcCCcch
Q 002930 394 VRALFDKIADLDMECRIRFILWFSHHLSNFQFIWPWEEWAYVLDLPKWAPQRVFVQEVLEREVRLSYWDKVKQSIENAPA 473 (864)
Q Consensus 394 ir~ly~~l~~mD~e~~~Rf~dWFS~HLSNF~F~W~W~eW~~~l~l~~~hPk~~Fir~vLeKeiRLSY~~RIk~slP~~~~ 473 (864)
+|+||+++++||++|++||+||||||||||+|+|+|+||.+|+++|.+|||++|+|++|+||+|||||+||++++| ..
T Consensus 397 ~r~lY~rldsm~~~c~dR~idWFShHLSNF~F~w~W~eW~~~l~~d~~~pk~~FvreviqkelrLsy~~rI~dslP--~~ 474 (759)
T KOG1104|consen 397 VRILYMRLDSMDTECFDRFIDWFSHHLSNFQFRWKWNEWADCLGLDFEHPKPNFVREVIQKELRLSYYQRIKDSLP--TL 474 (759)
T ss_pred HHHHHHHhccCCHHHHHHHHHHHHHHhccCcceechhhhhhhcCCCCcCcchhHHHHHHHHHHHHHHHHHHHHhhh--HH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999 48
Q ss_pred hhccCCCCCCCCccccCCCCccCchhHHHHHHHHHHhcCCCCHHHHHHHHHhh--ccCCCCchhHHHHHHHHHHHhccch
Q 002930 474 LEELLPPKGGPNFKYSMEDGRERSEEHALSAELTNKVKGRQTAREIIVWVEES--VYPIHGLGVTIKVVVQTLLDIGSKS 551 (864)
Q Consensus 474 ~~~llP~~p~P~~~y~~e~~~~~~~~~~~a~~l~~~lk~k~~~~ei~~~l~e~--~~~~~g~~~~i~vfvq~ll~~GsKS 551 (864)
+..++|++|+|+|+|.+|.++. .++..+|.++..++|.|++++++..+|+.. ....+++.++|.+||||+|++||||
T Consensus 475 ~~~l~P~~~~pny~y~~Ee~~~-~~~~~~~~~l~~~~~~k~~~e~~~~iLk~~~~~~~~~~n~~~i~lfvq~~l~lGSKS 553 (759)
T KOG1104|consen 475 LAKLLPPPPLPNYKYTDEEDPV-LPQSLVAVQLIVAFREKATAEEIVNILKSEDESEIGSFNRLKIILFVQTLLDLGSKS 553 (759)
T ss_pred HHHhCCCCCCCceeeecccCcc-ccchHHHHHHHHHHhccCCHHHHHHHHhcCccccccCCcceehhhHHHHHHHhccch
Confidence 9999999999999999997653 455568999999999999999999999921 2234567899999999999999999
Q ss_pred hhhHHHHHHHHHHHHHhhCCChHH-HHHHHHHHHHHHhhCCCcchhHHHHhhhccccChhhHHHhhcCccccccccccCc
Q 002930 552 FTHLITVLERYGQVISKICPDHDK-QLMLIEEVSLFWKNNTQNAAISIDRMMGYRLISNLAIVRWVFSPENIDQFHASDR 630 (864)
Q Consensus 552 fSH~~~~iery~~~lk~l~~~~~~-q~~il~~v~~~W~~~pQ~~~ivvDkll~~~Iv~p~~Vv~W~F~~~~~~~~~~~~~ 630 (864)
|||++++++||+++||+++.+++. |.++|++|++||++||||+++++|||++|+||+|.+||+|+|+++|.++|+. .|
T Consensus 554 fSH~f~~lek~~~vfk~l~~~~e~~q~~vl~~vft~Wk~n~Qm~~v~~Dkml~~~ii~~~aVv~WiF~~~m~~~~~r-~~ 632 (759)
T KOG1104|consen 554 FSHAFSALEKYHTVFKKLCEDSETKQIIVLEAVFTFWKANPQMGFVLTDKMLKYQIIDCSAVVRWIFSEEMVNEFTR-LY 632 (759)
T ss_pred hhhHHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHhcCchhhHHHHHHHhccccccHHHHHHHhcCHHhhhhHHH-HH
Confidence 999999999999999999987655 9999999999999999999999999999999999999999999999988875 99
Q ss_pred hHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhccccCCCCCCCCChhhhhHhHHhHhhhhhh
Q 002930 631 PWEVLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKLSLVDGEPVLGGNPARLSRLKLHAEKAKNE 710 (864)
Q Consensus 631 ~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 710 (864)
+||+||+|++|+++|+++++++++++.+++..++.+......+ +.+ +| ++.
T Consensus 633 ~wEil~~al~K~~~~~~~~~k~ie~~~e~~~~~~~~~~d~~~~-------------------~~~--~~-----~~~--- 683 (759)
T KOG1104|consen 633 LWEILHSALNKLNKHLNRSQKNIEEVTEKLETAEKSEIDLEDD-------------------LSA--ER-----DEI--- 683 (759)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhcccccchhhh-------------------hhh--hh-----hhh---
Confidence 9999999999999999999999999999876542221111111 000 00 122
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccCCcccccccccchhhhcccCCcccccccccCCCC
Q 002930 711 EISAKESLEAKEALFARAVEENEALYLSLYRNFSNVLMERLPDASRAGTLQDLKSTHADAMAVDLEEPSAMELDNENGRP 790 (864)
Q Consensus 711 ~~~~~~~~e~~~~~l~~a~~eqk~lfl~~~~~Fi~~L~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 (864)
.++.+|...+++|.|+-++|..|..+||+|+
T Consensus 684 ---~~e~~e~~~~~~E~~~~~~k~~~~~v~~k~~---------------------------------------------- 714 (759)
T KOG1104|consen 684 ---KEENVEGDPEDLEDANLKEKWLFFVVFQKFI---------------------------------------------- 714 (759)
T ss_pred ---hHHHhccChhhhhhhhHHHHHHHHHHhhhhH----------------------------------------------
Confidence 5566778888888899999999999999986
Q ss_pred CCCCCCCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhccCCCChhhHHH--HHhccC
Q 002930 791 KKSQSNGGSSGNVYNIGEKEQWCLSTLGYVKAFSRQYASEIWPHMEKLDAEVLSEDTHPLFRRA--VYSGLH 860 (864)
Q Consensus 791 ~~~~~~~~~~~~~~~~~~~~~W~~~~~g~~~~~~~~~~~~i~~~~~~l~~~~ft~~~~~~~~~~--~~~~~~ 860 (864)
++++.|..|++...+|+.++++++||+|+||+|.+. +|++++
T Consensus 715 ----------------------------~le~~f~~~~e~~~k~~~~i~~~~~te~l~psi~~~~~~f~~~~ 758 (759)
T KOG1104|consen 715 ----------------------------ILEAYFLEHEELAQKYSSTIENLVFTEDLDPSISNVFQQFVALR 758 (759)
T ss_pred ----------------------------HHHHHHHHHHHHHHHHHHHhhccccccccChHHHHHHHHHhhhc
Confidence 234556779999999999999999999999999998 676665
No 2
>PF09088 MIF4G_like: MIF4G like; InterPro: IPR015172 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 1", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=100.00 E-value=2.6e-62 Score=493.25 Aligned_cols=165 Identities=45% Similarity=0.904 Sum_probs=113.2
Q ss_pred CCCchhHHHHHHHHHHHHHhccccHHHHHHHhhcCC-------------------------CCCCchhhHHHHHHHHhhc
Q 002930 306 DMQPIDRFILEEYLLDVLLFFNGCRKECAFYMVNLP-------------------------VPFRYEYLMAETIFSQLLL 360 (864)
Q Consensus 306 ~~~~ier~liee~i~Dii~~f~~nRKecA~~Ll~lp-------------------------~t~k~E~~iVEtIfs~lf~ 360 (864)
+.++|+|++++++|.|||+.+++||||||++|+++| ++|++||+|||||||+||+
T Consensus 2 ~~~si~~~l~rd~i~Dii~~~~~NRke~A~~Ll~l~~~f~~~~F~~~~~~~~~l~~~~~~~~~~~~e~~ivE~ifs~mf~ 81 (191)
T PF09088_consen 2 PITSIAGFLLRDIIVDIIEILEFNRKECARQLLDLDCYFAPGTFKKRGTSFDQLREEDPSKSTWKIEDLIVETIFSQMFQ 81 (191)
T ss_dssp ------------------------------------------------------------SS---HHHHHHHHHHHHHT-
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCcHHHHHHHHHHHHHHh
Confidence 567899999999999999999999999999998853 4689999999999999999
Q ss_pred CCCCCCcchhHHHHHHHHHhcCCCCchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhhhcccCccccccccccccCCCC
Q 002930 361 LPQPPFKPIYYTLVIMDLCKALPGAFPAVVAGAVRALFDKIADLDMECRIRFILWFSHHLSNFQFIWPWEEWAYVLDLPK 440 (864)
Q Consensus 361 LP~p~~~~vYY~slLiELCK~~P~~iapvlgrAir~ly~~l~~mD~e~~~Rf~dWFS~HLSNF~F~W~W~eW~~~l~l~~ 440 (864)
||+|+++.+||+|||+||||++|++||||+|||||+||+|+++||+||++||+||||||||||||+|+|+||++|+++++
T Consensus 82 LP~p~~~~iyY~sllielCk~~P~~i~pv~~~air~ly~~l~~md~e~~~Rf~dWfS~hLSNF~f~W~W~eW~~~~~l~~ 161 (191)
T PF09088_consen 82 LPSPPHKLIYYHSLLIELCKLSPSAIPPVLGRAIRFLYRNLDSMDFELRDRFVDWFSHHLSNFGFQWKWDEWVDDLELPP 161 (191)
T ss_dssp SS--SS-HHHHHHHHHHHHHHSTTTHHHHHHHHHHHHHHGGGGB-HHHHHHHHHHHHHHHHTTTT---GGGGGGGTTS-T
T ss_pred CCCCCCchhHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHhcCCceeeHHHhhhhhhCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCchHHHHHHHHHHHHhhchhHHHHHhcCC
Q 002930 441 WAPQRVFVQEVLEREVRLSYWDKVKQSIEN 470 (864)
Q Consensus 441 ~hPk~~Fir~vLeKeiRLSY~~RIk~slP~ 470 (864)
.|||++|||++|+||+||||++|||++|||
T Consensus 162 ~~pk~~Fi~~~l~k~iRLSy~~rIk~~LPe 191 (191)
T PF09088_consen 162 LHPKRVFIREVLEKEIRLSYYDRIKESLPE 191 (191)
T ss_dssp TSHHHHHHHHHHHHHHHTS-HHHHHHHS--
T ss_pred cCCHHHHHHHHHHHHHhcccHHHHHHhCCC
Confidence 999999999999999999999999999995
No 3
>PF09090 MIF4G_like_2: MIF4G like; InterPro: IPR015174 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 2", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=100.00 E-value=5.1e-47 Score=404.67 Aligned_cols=243 Identities=35% Similarity=0.577 Sum_probs=202.4
Q ss_pred ccccCCCCccCchhHHHHHHHHHHhcCCCCHHHHHHHHHhhccCCCCc-----hhHHHHHHHHHHHhccchhhhHHHHHH
Q 002930 486 FKYSMEDGRERSEEHALSAELTNKVKGRQTAREIIVWVEESVYPIHGL-----GVTIKVVVQTLLDIGSKSFTHLITVLE 560 (864)
Q Consensus 486 ~~y~~e~~~~~~~~~~~a~~l~~~lk~k~~~~ei~~~l~e~~~~~~g~-----~~~i~vfvq~ll~~GsKSfSH~~~~ie 560 (864)
|+|.++ +.|+++.|++|.+++|+|++++|+.+++++...+..+. .+++++|+||+|++|||||||++++|+
T Consensus 1 fky~~e----~~P~~~~a~~l~~~ir~k~~~eei~~~l~~i~~~~~~~~~~~~~~~i~v~~q~ll~~GSkS~SH~~~~le 76 (253)
T PF09090_consen 1 FKYENE----SLPFHALAQKLLDLIRKKAPPEEISELLEEIEEPAEEHGSDFDKFVIDVFVQCLLHIGSKSFSHVLSALE 76 (253)
T ss_dssp -TTS-T----TSTTHHHHHHHHHHHHTT--HHHHHHHHTTS------------HHHHHHHHHHHHHHTTTSHHHHHHHHH
T ss_pred CCCCCC----CCccHHHHHHHHHHHHcCCCHHHHHHHHHhccccccccccchhhHHHHHHHHHHHHhcCchHHHHHHHHH
Confidence 688665 47899999999999999999999999999754433322 589999999999999999999999999
Q ss_pred HHHHHHHhh-CCChHHHHHHHHHHHHHHhhCCCcchhHHHHhhhccccChhhHHHhhcCccccccccccCchHHHHHHHH
Q 002930 561 RYGQVISKI-CPDHDKQLMLIEEVSLFWKNNTQNAAISIDRMMGYRLISNLAIVRWVFSPENIDQFHASDRPWEVLRNAV 639 (864)
Q Consensus 561 ry~~~lk~l-~~~~~~q~~il~~v~~~W~~~pQ~~~ivvDkll~~~Iv~p~~Vv~W~F~~~~~~~~~~~~~~WEil~~ti 639 (864)
||+++||.+ ++++++|.+||++|++||++||||+++|+|||++||||+|.+||+|+|++++....+++.|+||+|++|+
T Consensus 77 ry~~~Lk~l~~~~~~~q~~il~~v~~~W~~~~q~~~li~dkll~~~ii~~~~Vv~w~f~~~~~~~~~~~~~~wE~l~~tl 156 (253)
T PF09090_consen 77 RYKEVLKELEAESEEAQFWILDAVFRFWKNNPQMGFLIIDKLLNYGIISPSAVVNWVFSPENGNQELTRSYVWEILNRTL 156 (253)
T ss_dssp HTHHHHHHH-TSSHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-HHHHHHHHTSGGG-TTTTTSHHHHHHHHHHH
T ss_pred HHHHHHHHhccCChHHHHHHHHHHHHHHhcCCceehHHHHHHHhcCCCCHHHHHHHHcCccccccchhhchHHHHHHHHH
Confidence 999999999 7888999999999999999999999999999999999999999999999998434446799999999999
Q ss_pred HHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhccccCCCCCCCCChhhhhHhHHhHhhhhhhhhhHHHHHH
Q 002930 640 SKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKLSLVDGEPVLGGNPARLSRLKLHAEKAKNEEISAKESLE 719 (864)
Q Consensus 640 ~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 719 (864)
+|+++|++++++++++++. . + .+.. . .+++++
T Consensus 157 ~k~~~rv~~~~~~~~~~~~-------------~---e----------------~~~~---------~-------~~~~~~ 188 (253)
T PF09090_consen 157 RKVTKRVRQVRKELEEAKA-------------E---E----------------NSSE---------E-------DEEELE 188 (253)
T ss_dssp HHHHHHHHHHHHHHHHHH--------------------------------------------------------HHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcc-------------c---c----------------cchh---------h-------hhHHHH
Confidence 9999999999999888861 0 0 0000 0 156689
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhcCCCccCCcccccccccchhhhcccCCcccccccccCCCCCCCCCC
Q 002930 720 AKEALFARAVEENEALYLSLYRNFSNVL---MERLPDASRAGTLQDLKSTHADAMAVDLEEPSAMELDNENGRPKKSQSN 796 (864)
Q Consensus 720 ~~~~~l~~a~~eqk~lfl~~~~~Fi~~L---~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 796 (864)
.++++|++++.+||++|+.++++|+++| ++|..+|+.++.+
T Consensus 189 ~~~~~L~~~~~e~~~~l~~~~~~fv~~l~~~~~~~~~~~~~~~~------------------------------------ 232 (253)
T PF09090_consen 189 SLEEKLERALEEQKNLLLLIFQRFVMVLVIESEHLVECEQDLRD------------------------------------ 232 (253)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHT--------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccchhhhhHH------------------------------------
Confidence 9999999999999999999999999999 8888887776643
Q ss_pred CCCCCCcccccchhhH-HHHHHHHHHHHHHHH
Q 002930 797 GGSSGNVYNIGEKEQW-CLSTLGYVKAFSRQY 827 (864)
Q Consensus 797 ~~~~~~~~~~~~~~~W-~~~~~g~~~~~~~~~ 827 (864)
| .+.| |++++||+|+|+|+|
T Consensus 233 -------~----~~~W~~~~~~g~~k~~~rky 253 (253)
T PF09090_consen 233 -------W----DTRWLFRWYVGRLKSFLRKY 253 (253)
T ss_dssp -------S----S-HH-HHHHHHHHHHHHHHT
T ss_pred -------h----ccCcHHHHHHHHHHHHHHhC
Confidence 3 4999 999999999999998
No 4
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=99.58 E-value=2.6e-14 Score=145.75 Aligned_cols=171 Identities=26% Similarity=0.411 Sum_probs=143.0
Q ss_pred chhhHhhhccCCCCCCCCCchHhhHHHHHHHHHhhhccccCcHHHHHHHHHHhCCCCchHHHHHHHHHhcCChhHHHHHH
Q 002930 4 WKNLLLKIGDNCPEYGNSDDLKDHIETCFGVIRRELEHSSDDVPHYIINCAEQIPHKIPLYGTLVGLLNLENEDFVKKVV 83 (864)
Q Consensus 4 ~~~li~riGek~~~~~~~ss~e~~ie~La~~l~~el~~~~~~il~~l~~cv~e~P~K~p~YAtLVgllN~kn~~~g~~iv 83 (864)
.++++-|+++. .++..++.+.+.... -++.++.+++++++++..+|+++|+||+|++.+|..+++||+.++
T Consensus 4 v~~~lnkLs~~--------n~~~~~~~l~~~~~~-~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll 74 (200)
T smart00543 4 VKGLINKLSPS--------NFESIIKELLKLNNS-DKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLL 74 (200)
T ss_pred HHHHHhhCCHH--------HHHHHHHHHHHHHcc-CHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566666522 444444444444432 245679999999999999999999999999999999999999999
Q ss_pred HHHHHHHHH---HHhcCCchhHHHHHHHHhhcccccccCcccHHHHHHHHHHhhhhcccccCCCChhhhhhhHHHHHHHh
Q 002930 84 ETTQRKFQD---ALDSGNCDRIRILMRFLTVMMCSKILQPGSLVVVFETLLSSAATTVDEDKGNPSWQARADFYVTCILS 160 (864)
Q Consensus 84 e~~~~~lq~---~L~~g~w~~~klllRFLa~Lvn~~Vi~~~sl~~ll~~Ll~~a~~~~~~e~~~~~~q~r~D~~v~~vL~ 160 (864)
+.+...|+. ..+.+.|++++..+||||+|++.++++...+++++..|++.. . +.+ ..|+|+.+.|++.
T Consensus 75 ~~~~~~f~~~~e~~~~~~~~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~ll~~~----~-~~~----~~~~~~~ve~l~~ 145 (200)
T smart00543 75 ERLQEEFEKGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDL----T-KLD----PPRSDFSVECLLS 145 (200)
T ss_pred HHHHHHHHHHHHHHHHHhhhhHHhHHHHHHHHHHcccCcHHHHHHHHHHHHhcc----C-CCC----CCCcHHHHHHHHH
Confidence 999999999 667788999999999999999999999999999999999742 1 111 1278899999999
Q ss_pred hhhhccHHhh-hhCHHHHHHHHHHHHHHHhhcc
Q 002930 161 CLPWGGAELI-EQVPEEIERVMAGLEAYLSIRR 192 (864)
Q Consensus 161 ~LP~~G~eL~-e~~~e~Le~ll~~ie~y~~~R~ 192 (864)
.|+++|..|. ...+..++.+++.++.|+..++
T Consensus 146 lL~~~G~~l~~~~~~~~~~~~l~~l~~~~~~~~ 178 (200)
T smart00543 146 LLPTCGKDLEREKSPKLLDEILERLQDYLLKKD 178 (200)
T ss_pred HHHHhhHHHcCcccHHHHHHHHHHHHHHHhccc
Confidence 9999999999 7899999999999999998775
No 5
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=99.44 E-value=2e-11 Score=136.90 Aligned_cols=384 Identities=15% Similarity=0.250 Sum_probs=234.7
Q ss_pred cccCcHHHHHHHHHHhCCCCchHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHhcCCchhHHHHHHHHhhcccccccCc
Q 002930 41 HSSDDVPHYIINCAEQIPHKIPLYGTLVGLLNLENEDFVKKVVETTQRKFQDALDSGNCDRIRILMRFLTVMMCSKILQP 120 (864)
Q Consensus 41 ~~~~~il~~l~~cv~e~P~K~p~YAtLVgllN~kn~~~g~~ive~~~~~lq~~L~~g~w~~~klllRFLa~Lvn~~Vi~~ 120 (864)
..++.+++.+++.+..-|..+|+||+||+|+|+|.|.+|+.++.+++.+|+..+..+++-.|-.++.|+|||+|+.|.+.
T Consensus 194 rgRgl~crsv~~aq~asp~ft~vyaALvAviNskfP~IgElLlkrLilqf~r~f~RnDk~~c~~~~kfiahLinq~VahE 273 (739)
T KOG2140|consen 194 RGRGLLCRSVMQAQAASPGFTPVYAALVAVINSKFPQIGELLLKRLILQFKRSFRRNDKVSCLNASKFIAHLINQQVAHE 273 (739)
T ss_pred hccchhHHHHHHHHhcCCCCcHHHHHHHHHHccCCchHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHH
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHhhhhcccccCCCChhhhhhhHHHHHHHhhhhhccHHhhhhCHHHHHHHHHHHHHHHhhcccCCCCCcc
Q 002930 121 GSLVVVFETLLSSAATTVDEDKGNPSWQARADFYVTCILSCLPWGGAELIEQVPEEIERVMAGLEAYLSIRRHTSDTGLS 200 (864)
Q Consensus 121 ~sl~~ll~~Ll~~a~~~~~~e~~~~~~q~r~D~~v~~vL~~LP~~G~eL~e~~~e~Le~ll~~ie~y~~~R~~~~~~ll~ 200 (864)
--.++++--||+. +++++ +++ +..-+--||..|.+-.+-.++.|+++++.-+ ....
T Consensus 274 Iv~Leil~lLLe~-------PTddS-vev--------aI~flkecGakL~~VSpr~~n~IfErlR~IL-he~E------- 329 (739)
T KOG2140|consen 274 IVALEILTLLLER-------PTDDS-VEV--------AIAFLKECGAKLAEVSPRALNGIFERLRYIL-HEGE------- 329 (739)
T ss_pred HHHHHHHHHHhcC-------CCCch-HHH--------HHHHHHHHHHHHHHhChHHHhHHHHHHHHHH-hHhh-------
Confidence 9899998888763 56655 222 3444667899999999999999999987643 1110
Q ss_pred cccCCCCCCCCcchHhHHHHHHHHHHHHHhCCCcccCCCCCcchhhhhhccCC---CcCCCCCCCCCC--CC-CCCCC--
Q 002930 201 FFEEDDESGKGLVEKDFLEDLWHRVQALSSNGWKLDSVPRPHLSFEAQLVSGK---SHEFGPISCPEQ--PD-VPTAV-- 272 (864)
Q Consensus 201 ~~~~~~~~~~~~~~~~~L~~Lw~ql~~L~~~~W~~~~ipRpy~~f~~~L~~~~---~H~lp~i~~P~~--~~-~~~~~-- 272 (864)
-+..+.-+..-+=+-++++|+.-..-++-++ |++.. .|.++ +-+. |+ ....|
T Consensus 330 -------------ld~rvqy~iEtlf~iRkdkfk~~p~v~~~LD----lvee~dq~tH~l~---l~de~dpe~~L~vFk~ 389 (739)
T KOG2140|consen 330 -------------LDRRVQYMIETLFQIRKDKFKSHPAVLEELD----LVEEEDQITHSLS---LEDEDDPEKELGVFKK 389 (739)
T ss_pred -------------HHHHHHHHHHHHHHHHHHhhccCCccccccC----ccchhhheeeeee---cccccChhhhhccccc
Confidence 1122222333444456777765322222111 22221 24332 0000 00 00000
Q ss_pred -CCcccCCccccccccCCccccccccccCCCC-------------C----------------CCCCchhHHHHHHHHHHH
Q 002930 273 -SGITHGKQKHDAELKYPQRIRRLNIFPASKS-------------E----------------VDMQPIDRFILEEYLLDV 322 (864)
Q Consensus 273 -~~~~~~~~~~~~~~~yP~~~~~frlf~~~~~-------------~----------------~~~~~ier~liee~i~Di 322 (864)
|+. .+.+.+|-. ..-.++..++. + .+....+-.-++.-|.=+
T Consensus 390 dp~f------~ene~kyda--ikkeiLgn~dsen~d~~~~s~E~~~eee~e~~ee~~e~~qI~D~T~~Nlv~frr~IYLt 461 (739)
T KOG2140|consen 390 DPNF------EENEEKYDA--IKKEILGNEDSENEDDEDGSSEDDDEEEDESVEEDEEKLQIIDMTETNLVNFRRTIYLT 461 (739)
T ss_pred CccH------HHHHHHHHH--HHHHHhcCCcccccccccccccccccccccccccccccceeeccccchhHHhhhhheee
Confidence 000 000000000 00001111111 0 011222222334433332
Q ss_pred HHhccccHHHHHHHhhcC--CCCCC--chhhHHHHHHHHhhcCCCCCCcchhHHHHHHHHHhcCCCCchHHHHHHHHHHH
Q 002930 323 LLFFNGCRKECAFYMVNL--PVPFR--YEYLMAETIFSQLLLLPQPPFKPIYYTLVIMDLCKALPGAFPAVVAGAVRALF 398 (864)
Q Consensus 323 i~~f~~nRKecA~~Ll~l--p~t~k--~E~~iVEtIfs~lf~LP~p~~~~vYY~slLiELCK~~P~~iapvlgrAir~ly 398 (864)
|. =..+=.|||.-|+-+ |...+ +=++||++-.-+ ....=||+-|.-..|++.- .--..+.+++.--|
T Consensus 462 i~-SSldfeEaaHKLLKmkip~~q~~elc~mii~cc~Qe-------rTy~kFYglL~eRfc~l~r-~~q~~fe~~f~q~Y 532 (739)
T KOG2140|consen 462 IQ-SSLDFEEAAHKLLKMKIPESQEKELCNMIIDCCAQE-------RTYEKFYGLLGERFCMLHR-EWQEAFEKCFKQQY 532 (739)
T ss_pred ee-ccCcHHHHHHHHHhccCCchhhHHHHHHHHHHhhhH-------HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence 22 134567899999875 43322 345667765332 1224588888888999864 56678999999999
Q ss_pred hcCCCCcHHHHHHHHHHHHhhhcccCccccccccccccCC---CCCCchHHHHHHHHHHHHhhchhHHHHHhcCCc---c
Q 002930 399 DKIADLDMECRIRFILWFSHHLSNFQFIWPWEEWAYVLDL---PKWAPQRVFVQEVLEREVRLSYWDKVKQSIENA---P 472 (864)
Q Consensus 399 ~~l~~mD~e~~~Rf~dWFS~HLSNF~F~W~W~eW~~~l~l---~~~hPk~~Fir~vLeKeiRLSY~~RIk~slP~~---~ 472 (864)
..|..++..-.+-++-+|+|-||-=-. +|+= -.|+.+ +....-|.||+=+..-.+--=-.+.+..-|-++ +
T Consensus 533 stIhr~EtnkLRnlakffahLlstd~l--pw~v-l~~ikLTEEdTtsssRIfiKilFqELve~lGl~~L~~RL~dptl~~ 609 (739)
T KOG2140|consen 533 STIHRYETNKLRNLAKFFAHLLSTDAL--PWDV-LACIKLTEEDTTSSSRIFIKILFQELVEALGLDKLNERLNDPTLQP 609 (739)
T ss_pred HHHHHHhHHHHHHHHHHHHHHhccccc--chHH-HHHhhcccccCCccceehHHHHHHHHHHHhChHHHHHHhcCcchhh
Confidence 999999999888899999999985433 4432 223222 333334888876665544322223333333221 3
Q ss_pred hhhccCCCCCCCCccc
Q 002930 473 ALEELLPPKGGPNFKY 488 (864)
Q Consensus 473 ~~~~llP~~p~P~~~y 488 (864)
-+++++|-...-+.+|
T Consensus 610 ~l~glFP~dnp~n~Rf 625 (739)
T KOG2140|consen 610 KLEGLFPRDNPRNTRF 625 (739)
T ss_pred hhhccCcCCCccccee
Confidence 6788888763334444
No 6
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=99.37 E-value=6.9e-12 Score=127.93 Aligned_cols=173 Identities=18% Similarity=0.316 Sum_probs=144.9
Q ss_pred chhhHhhhccCCCCCCCCCchHhhHHHHHHHHHhhhccccCcHHHHHHHHHHhCCCCchHHHHHHHHHhcCCh-hHHHHH
Q 002930 4 WKNLLLKIGDNCPEYGNSDDLKDHIETCFGVIRRELEHSSDDVPHYIINCAEQIPHKIPLYGTLVGLLNLENE-DFVKKV 82 (864)
Q Consensus 4 ~~~li~riGek~~~~~~~ss~e~~ie~La~~l~~el~~~~~~il~~l~~cv~e~P~K~p~YAtLVgllN~kn~-~~g~~i 82 (864)
.+++|-|+.+. .++.-++.+.+....+-++..+.+++++++++.++|+++|+||.|++.++...+ +|+..+
T Consensus 4 v~~~lnklt~~--------n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~l 75 (209)
T PF02854_consen 4 VRGILNKLTPS--------NFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLL 75 (209)
T ss_dssp HHHHHHHCSST--------THHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred HHHHHHHCCHH--------HHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHH
Confidence 45666666633 555656665555554434456899999999999999999999999999999999 999999
Q ss_pred HHHHHHHHHH--------HHhcCCchhHHHHHHHHhhcccccccCcccHHHHHHHHHHhhhhcccccCCCChhhhhhhHH
Q 002930 83 VETTQRKFQD--------ALDSGNCDRIRILMRFLTVMMCSKILQPGSLVVVFETLLSSAATTVDEDKGNPSWQARADFY 154 (864)
Q Consensus 83 ve~~~~~lq~--------~L~~g~w~~~klllRFLa~Lvn~~Vi~~~sl~~ll~~Ll~~a~~~~~~e~~~~~~q~r~D~~ 154 (864)
++++...|+. ......+.+.+..+||+|+|.+.+|++...++.++..|++.... +. . +.+.+..
T Consensus 76 l~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~----~~--~--~~~~~~~ 147 (209)
T PF02854_consen 76 LNRCQEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSDGTD----EC--Q--PPPDEEN 147 (209)
T ss_dssp HHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSH----HC--C--HHTCHHH
T ss_pred HHHHHHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhcccc----cc--c--CCCcHhH
Confidence 9999999999 56778899999999999999999999999999999999985321 10 0 4567789
Q ss_pred HHHHHhhhhhccHHhh--hhCHHHHHHHHHHHHHHHhhcc
Q 002930 155 VTCILSCLPWGGAELI--EQVPEEIERVMAGLEAYLSIRR 192 (864)
Q Consensus 155 v~~vL~~LP~~G~eL~--e~~~e~Le~ll~~ie~y~~~R~ 192 (864)
+.|++..|+++|+.|. +..+..++.++..++.|.....
T Consensus 148 ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~~~~~~~~ 187 (209)
T PF02854_consen 148 IECLCTLLKTCGKKLENSEESPKALDEIFERLQKYANSKK 187 (209)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhhc
Confidence 9999999999999999 8888999999999999987753
No 7
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=94.42 E-value=4.6 Score=49.08 Aligned_cols=130 Identities=11% Similarity=0.177 Sum_probs=99.4
Q ss_pred HHHHHHHHHhCCCCchHHHHHHHHHhcCC-hhHHHHHHHHHHHHHHHHHhcCCch-----hHHHHHHHHhhcccccccCc
Q 002930 47 PHYIINCAEQIPHKIPLYGTLVGLLNLEN-EDFVKKVVETTQRKFQDALDSGNCD-----RIRILMRFLTVMMCSKILQP 120 (864)
Q Consensus 47 l~~l~~cv~e~P~K~p~YAtLVgllN~kn-~~~g~~ive~~~~~lq~~L~~g~w~-----~~klllRFLa~Lvn~~Vi~~ 120 (864)
+++++.--.-+-.-+..||+|..-|.+.- -++|.-+++.++..|-.+++.-.-. .+-.++-||+.|+|-+|+++
T Consensus 363 ~~~~~~~~~~ld~~~~~y~AL~~~l~~~vg~eigahf~q~~ve~f~~~~~~~~~~~~~~K~~~Nl~~~l~ylynF~ivs~ 442 (822)
T KOG2141|consen 363 LKALLGPFRLLDSLLTTYAALAAMLHTMVGNEIGAHFLQTFVEDFLKSYKEEEEMDLKDKSLNNIVLFLSYLYNFGIVSC 442 (822)
T ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHhhcccH
Confidence 34444333444455678999999999864 4799999988888888888653322 36677999999999999999
Q ss_pred ccHHHHHHHHHHhhhhcccccCCCChhhhhhhHHHHHHHhhhhhccHHhhhhCHHHHHHHHHHHHHHHhhcc
Q 002930 121 GSLVVVFETLLSSAATTVDEDKGNPSWQARADFYVTCILSCLPWGGAELIEQVPEEIERVMAGLEAYLSIRR 192 (864)
Q Consensus 121 ~sl~~ll~~Ll~~a~~~~~~e~~~~~~q~r~D~~v~~vL~~LP~~G~eL~e~~~e~Le~ll~~ie~y~~~R~ 192 (864)
.-++.++..|...- + + .-+.++|.-|-++|.-|-...|-.+..++..+..-+++-+
T Consensus 443 ~LiydiI~kl~~~l-~----e-----------~~ve~ll~ii~~~G~~LRkDDp~alk~~i~eiq~~a~~a~ 498 (822)
T KOG2141|consen 443 SLIYDIIRKLAENL-N----E-----------TNVEALLTIIANCGFSLRKDDPLALKDIITEIQSKAASAK 498 (822)
T ss_pred HHHHHHHHHHHhch-h----h-----------hhHHHHHHHHHHccchhcCCChHHHHHHHHHHHHHhhcCC
Confidence 99999999998631 1 2 1456678888889999999999999999999888776654
No 8
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=93.93 E-value=0.16 Score=63.03 Aligned_cols=127 Identities=14% Similarity=0.233 Sum_probs=97.1
Q ss_pred ccCcHHHHHHHHHHhCCCCchHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHhcCCc--hhHH-HHHHHHhhccccccc
Q 002930 42 SSDDVPHYIINCAEQIPHKIPLYGTLVGLLNLENEDFVKKVVETTQRKFQDALDSGNC--DRIR-ILMRFLTVMMCSKIL 118 (864)
Q Consensus 42 ~~~~il~~l~~cv~e~P~K~p~YAtLVgllN~kn~~~g~~ive~~~~~lq~~L~~g~w--~~~k-lllRFLa~Lvn~~Vi 118 (864)
.|+.+++.++......=...|+|+.+|+.+..-++++..++|..+-..|+..+.+.+- ...| .++||++.|+--++|
T Consensus 459 ~RkrLvKal~~vprt~ldllPyYsRlVAtl~~~M~dvat~lv~~L~~eFr~~~hkK~q~~ietk~~~VrfIsEL~KF~lv 538 (1128)
T KOG2051|consen 459 NRKRLVKALFVVPRTRLDLLPYYSRLVATLSKCMPDVATELVTMLRKEFRSHLHKKAQINIETKLKIVRFISELCKFQLV 538 (1128)
T ss_pred HHHHHHHhhhcccchhhhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHhhhhhCcc
Confidence 4578888888888888899999999999999999999999999999999999987632 3333 569999999999999
Q ss_pred CcccHHHHHHHHHHhhhhcccccCCCChhhhhhhHHHHHHHhhhhhccHHhhhhCHH--HHHHHHHHH
Q 002930 119 QPGSLVVVFETLLSSAATTVDEDKGNPSWQARADFYVTCILSCLPWGGAELIEQVPE--EIERVMAGL 184 (864)
Q Consensus 119 ~~~sl~~ll~~Ll~~a~~~~~~e~~~~~~q~r~D~~v~~vL~~LP~~G~eL~e~~~e--~Le~ll~~i 184 (864)
+...+|.-|+.|+.- -++ .+. =++|+| |=-+|++|+..-.. .+..+++.|
T Consensus 539 ~~~~if~cLk~ll~d-------F~~-hnI------Em~c~l--LE~~GrfLlr~pEt~lrM~~~Le~i 590 (1128)
T KOG2051|consen 539 PKFEIFSCLKMLLND-------FTH-HNI------EMACVL--LESCGRFLLRSPETKLRMRVFLEQI 590 (1128)
T ss_pred ChHHHHHHHHHHHHh-------ccc-ccH------HHHHHH--HHhcchhhhcChhHHHHHHHHHHHH
Confidence 999999999999763 111 112 234444 34579998875332 345555553
No 9
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=78.11 E-value=18 Score=33.63 Aligned_cols=87 Identities=15% Similarity=0.252 Sum_probs=66.5
Q ss_pred ccHHHHHHHhhcCCCCCCchhhHHHHHHHHhhcCCCCCCcchhHHHHHHHHHhcCCCCchHHHHHHHHHHHhcCCCCcHH
Q 002930 328 GCRKECAFYMVNLPVPFRYEYLMAETIFSQLLLLPQPPFKPIYYTLVIMDLCKALPGAFPAVVAGAVRALFDKIADLDME 407 (864)
Q Consensus 328 ~nRKecA~~Ll~lp~t~k~E~~iVEtIfs~lf~LP~p~~~~vYY~slLiELCK~~P~~iapvlgrAir~ly~~l~~mD~e 407 (864)
++-.|++.-+..++.+ +..+-+|..++...+.- .....=||..|+..||+... ..+..|.+++.-+|+.++.+.++
T Consensus 16 ~D~~ea~~~l~~L~~~-~~~~~vv~~~i~~~le~--~~~~~~~~~~Ll~~L~~~~~-~~~~~~~~~f~~~~~~l~dl~~D 91 (113)
T smart00544 16 GDTDEAVHCLLELKLP-EQHHEVVKVLLTCALEE--KRTYREMYSVLLSRLCQANV-ISTKQFEKGFWRLLEDIEDLELD 91 (113)
T ss_pred CCHHHHHHHHHHhCCC-cchHHHHHHHHHHHHcC--CccHHHHHHHHHHHHHHcCC-cCHHHHHHHHHHHHhhChhhhcc
Confidence 5788899999888766 56778888888888863 22334689999999999865 56789999999999999987663
Q ss_pred ---HHHHHHHHHHh
Q 002930 408 ---CRIRFILWFSH 418 (864)
Q Consensus 408 ---~~~Rf~dWFS~ 418 (864)
....++..+++
T Consensus 92 ~P~a~~~la~~~a~ 105 (113)
T smart00544 92 IPNAWRNLAEFVAR 105 (113)
T ss_pred cccHHHHHHHHHHH
Confidence 45555555544
No 10
>KOG1760 consensus Molecular chaperone Prefoldin, subunit 4 [Posttranslational modification, protein turnover, chaperones]
Probab=71.49 E-value=38 Score=32.83 Aligned_cols=95 Identities=22% Similarity=0.339 Sum_probs=58.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhccccCC--CCCC---CCCh--hhhhHhHHhHhhhh
Q 002930 636 RNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKLSLVDG--EPVL---GGNP--ARLSRLKLHAEKAK 708 (864)
Q Consensus 636 ~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~--~~~~~~~~~~~~~~ 708 (864)
-|-+.+.+.|+.++..+++.+|++++..+.|... . .+.+. .+.+ |+-- -..+.+. +.-+
T Consensus 22 iN~Fsrl~~R~~~lk~dik~~k~~~enledA~~E----i-------eL~Dedd~~Ip~~vGdvF~~~~~~~~~---~~LE 87 (131)
T KOG1760|consen 22 INEFSRLNSRKDDLKADIKEAKTEIENLEDASNE----I-------ELLDEDDEDIPFKVGDVFIHVKLDKLQ---DQLE 87 (131)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhh----H-------hhcCccccccceehhhhheeccHHHHH---HHHH
Confidence 4567789999999999999999988766544422 2 11111 1110 1100 0011111 2222
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002930 709 NEEISAKESLEAKEALFARAVEENEALYLSLYRNFS 744 (864)
Q Consensus 709 ~~~~~~~~~~e~~~~~l~~a~~eqk~lfl~~~~~Fi 744 (864)
+...+++++++.++.+++.-.+.-.+|=-.+|.+|=
T Consensus 88 e~ke~l~k~i~~les~~e~I~~~m~~LK~~LYaKFg 123 (131)
T KOG1760|consen 88 EKKETLEKEIEELESELESISARMDELKKVLYAKFG 123 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 234557888888888888888888888888899883
No 11
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=67.92 E-value=1.5e+02 Score=38.26 Aligned_cols=145 Identities=17% Similarity=0.304 Sum_probs=94.7
Q ss_pred CcHHHHHHHHHHhCCCCc-----hHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHhcCC---chhHHHHHHHHhhcccc
Q 002930 44 DDVPHYIINCAEQIPHKI-----PLYGTLVGLLNLENEDFVKKVVETTQRKFQDALDSGN---CDRIRILMRFLTVMMCS 115 (864)
Q Consensus 44 ~~il~~l~~cv~e~P~K~-----p~YAtLVgllN~kn~~~g~~ive~~~~~lq~~L~~g~---w~~~klllRFLa~Lvn~ 115 (864)
..+-.+++.|.+. |+|+ ++.|.|++=|-+-.++||=-||+.+.+.++-.|.-++ -.+.....|||+.|.|-
T Consensus 662 ~e~~~yli~~~~k-~w~iky~~i~~lA~llaGL~~y~~~fvi~VID~vlE~Ir~glEin~~~~nQrriA~aryL~ELynf 740 (1128)
T KOG2051|consen 662 PEVKQYLISCFSK-PWKIKYQNIHALASLLAGLSSYHPEFVIHVIDHVLEDIRPGLEINDYVSNQRRIALARYLGELYNF 740 (1128)
T ss_pred HHHHHHHHHHhhh-hhccccccHHHHHHHHHHHHhhchhhhhhhHHHHHHHHHhhhhcCcHHHHHHHHHHHHHHHHHhhh
Confidence 3466777777665 6654 5678887777788999999999999999999998544 34566789999999999
Q ss_pred cccCcccHHHHHHHHHHhhhhcc-cccCCCChhhhhhhHHHHHHHhhh-hhccHHhhhhCHHHHHHHHHHHHHHHhhcc
Q 002930 116 KILQPGSLVVVFETLLSSAATTV-DEDKGNPSWQARADFYVTCILSCL-PWGGAELIEQVPEEIERVMAGLEAYLSIRR 192 (864)
Q Consensus 116 ~Vi~~~sl~~ll~~Ll~~a~~~~-~~e~~~~~~q~r~D~~v~~vL~~L-P~~G~eL~e~~~e~Le~ll~~ie~y~~~R~ 192 (864)
.++..+-|+..|=.++....... ....-+|--..=+-.+|-++|.++ ||+-+ .....-+...+..++.|+-..+
T Consensus 741 emvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV~~lL~tc~~yf~r---gs~kkkl~~fL~~fq~Y~~iKk 816 (1128)
T KOG2051|consen 741 EMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLVCMLLQTCGPYFTR---GSTKKKLDQFLVAFQRYILIKK 816 (1128)
T ss_pred hhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHHHHHHHHccccccc---chhHHHHHHHHHHHHHHhhccc
Confidence 99999888877766665432110 000011100111223444445544 33321 1223467888889999987765
No 12
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=67.13 E-value=61 Score=31.73 Aligned_cols=26 Identities=19% Similarity=0.317 Sum_probs=13.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhhh
Q 002930 635 LRNAVSKTYNRICDLRKEIISLKKGV 660 (864)
Q Consensus 635 l~~ti~kv~~rv~~~~~~l~~~~~~~ 660 (864)
|.+++.-|.+++.++...|+++|+.+
T Consensus 41 m~~A~~~v~kql~~vs~~l~~tKkhL 66 (126)
T PF07889_consen 41 MSDAVASVSKQLEQVSESLSSTKKHL 66 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555555544
No 13
>PRK11637 AmiB activator; Provisional
Probab=65.90 E-value=2.2e+02 Score=33.30 Aligned_cols=33 Identities=15% Similarity=-0.014 Sum_probs=20.8
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002930 709 NEEISAKESLEAKEALFARAVEENEALYLSLYR 741 (864)
Q Consensus 709 ~~~~~~~~~~e~~~~~l~~a~~eqk~lfl~~~~ 741 (864)
.+...++.+++..+++++..+...+...-..++
T Consensus 103 ~ei~~l~~eI~~~q~~l~~~~~~l~~rlra~Y~ 135 (428)
T PRK11637 103 KQIDELNASIAKLEQQQAAQERLLAAQLDAAFR 135 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456666666777776666666666666555
No 14
>COG4372 Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]
Probab=65.48 E-value=46 Score=38.07 Aligned_cols=38 Identities=29% Similarity=0.369 Sum_probs=22.4
Q ss_pred HhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhc
Q 002930 644 NRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKL 681 (864)
Q Consensus 644 ~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 681 (864)
-...+++.+|..+|.++..++.++..++.|++.+.+.+
T Consensus 74 fqlddi~~qlr~~rtel~~a~~~k~~~e~er~~~~~El 111 (499)
T COG4372 74 FQLDDIRPQLRALRTELGTAQGEKRAAETEREAARSEL 111 (499)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456666666666666666666666665555544433
No 15
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=64.47 E-value=30 Score=32.09 Aligned_cols=100 Identities=16% Similarity=0.290 Sum_probs=70.1
Q ss_pred HHHHHHHH-hc-cccHHHHHHHhhcCCCCCCchhhHHHHHHHHhhcCCCCCCcchhHHHHHHHHHhcCCCCchHHHHHHH
Q 002930 317 EYLLDVLL-FF-NGCRKECAFYMVNLPVPFRYEYLMAETIFSQLLLLPQPPFKPIYYTLVIMDLCKALPGAFPAVVAGAV 394 (864)
Q Consensus 317 e~i~Dii~-~f-~~nRKecA~~Ll~lp~t~k~E~~iVEtIfs~lf~LP~p~~~~vYY~slLiELCK~~P~~iapvlgrAi 394 (864)
..+..++. +| .++-+|+...+..+..+ +...-+|..++...+.- .+..-=||+.|+..||+.. ..-...+.+|+
T Consensus 3 k~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~vv~~~l~~~le~--~~~~r~~~~~Ll~~L~~~~-~~~~~~~~~gf 78 (113)
T PF02847_consen 3 KKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHEVVKVILECALEE--KKSYREYYSKLLSHLCKRK-LISKEQFQEGF 78 (113)
T ss_dssp HHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHHHHHHHHHHHHTS--SHHHHHHHHHHHHHHHHTT-SS-HHHHHHHH
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHHHHHHHHHHHhhc--cHHHHHHHHHHHHHHHhcC-CCCHHHHHHHH
Confidence 33444443 33 36788899988887666 67788999999999973 2333468999999999964 35567999999
Q ss_pred HHHHhcCCCCcHH---HHHHHHHHHHhhh
Q 002930 395 RALFDKIADLDME---CRIRFILWFSHHL 420 (864)
Q Consensus 395 r~ly~~l~~mD~e---~~~Rf~dWFS~HL 420 (864)
..+++.++++... ....++..+++=+
T Consensus 79 ~~~l~~l~Dl~~D~P~~~~~la~~~~~~i 107 (113)
T PF02847_consen 79 EDLLESLEDLELDIPKAPEYLAKFLARLI 107 (113)
T ss_dssp HHHHHHHHHHHHHSTTHHHHHHHHHHHHH
T ss_pred HHHHhHhhhccccchHHHHHHHHHHHHHH
Confidence 9999999986666 5555555555533
No 16
>PF05546 She9_MDM33: She9 / Mdm33 family; InterPro: IPR008839 Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis []. The yeast Mdm33 protein assembles into an oligomeric complex in the inner membrane where it performs homotypic protein-protein interactions. It has been suggested that Mdm33 plays a distinct role, possibly involved in fission of the mitochondrial inner membrane [].
Probab=58.91 E-value=1.6e+02 Score=31.30 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=21.4
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 002930 637 NAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELE 675 (864)
Q Consensus 637 ~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 675 (864)
+.|.++...|.....++.++|+.+..|..+...|-..+.
T Consensus 32 s~Ie~LK~~i~~~E~~l~~~r~~~~~aK~~Y~~ai~~Rs 70 (207)
T PF05546_consen 32 SEIEKLKKSIEELEDELEAARQEVREAKAAYDDAIQQRS 70 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555556666666666666655555555544444443
No 17
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=57.89 E-value=60 Score=33.78 Aligned_cols=38 Identities=32% Similarity=0.405 Sum_probs=21.0
Q ss_pred ccCchHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHH
Q 002930 627 ASDRPWEVLRNAVSKTYNRICDLRKEIISLKKGVTLAE 664 (864)
Q Consensus 627 ~~~~~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~ 664 (864)
++.|.|.-=+.+..+...++..+.++++++++++...+
T Consensus 52 ssn~YWsFps~~~~~~~~~~~~l~~~~~~~~~~i~~l~ 89 (188)
T PF03962_consen 52 SSNYYWSFPSQAKQKRQNKLEKLQKEIEELEKKIEELE 89 (188)
T ss_pred CeeEEEecChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566655555555555555556666666655554433
No 18
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=57.64 E-value=55 Score=27.55 Aligned_cols=43 Identities=26% Similarity=0.384 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 002930 634 VLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEA 676 (864)
Q Consensus 634 il~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 676 (864)
-|.+=|..++.+|.++..++..+|..+..|.+++++|...+|.
T Consensus 7 ~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN 49 (56)
T PF04728_consen 7 QLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDN 49 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566677888899999999999998887777777777666643
No 19
>PRK10884 SH3 domain-containing protein; Provisional
Probab=57.38 E-value=95 Score=32.89 Aligned_cols=28 Identities=14% Similarity=0.240 Sum_probs=19.7
Q ss_pred HHHhHHHHHHHHHHHHhhhhHHHHHHHH
Q 002930 642 TYNRICDLRKEIISLKKGVTLAEEAAAK 669 (864)
Q Consensus 642 v~~rv~~~~~~l~~~~~~~~~~~~~~~~ 669 (864)
+..|+.++++++++++.+++.++.....
T Consensus 91 ~~~rlp~le~el~~l~~~l~~~~~~~~~ 118 (206)
T PRK10884 91 LRTRVPDLENQVKTLTDKLNNIDNTWNQ 118 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 5567778888888888877766554443
No 20
>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]
Probab=52.64 E-value=46 Score=37.24 Aligned_cols=114 Identities=17% Similarity=0.279 Sum_probs=85.3
Q ss_pred HHHHHHhcCCCCHHHHHHHHHhhccCCCCc-hhHHHHHHHHHHHhccchh------hhHHHHHHHHHHHHHhhCCChHHH
Q 002930 504 AELTNKVKGRQTAREIIVWVEESVYPIHGL-GVTIKVVVQTLLDIGSKSF------THLITVLERYGQVISKICPDHDKQ 576 (864)
Q Consensus 504 ~~l~~~lk~k~~~~ei~~~l~e~~~~~~g~-~~~i~vfvq~ll~~GsKSf------SH~~~~iery~~~lk~l~~~~~~q 576 (864)
+.|.+.+-...+..||+.++++....++-+ ..+|-+++.|+...+.=|= ..++.-+..|.++|..++.+...+
T Consensus 259 ~~L~~q~s~e~p~~evi~~VKee~k~~nlPe~eVi~ivWs~iMsaveWnKkeelva~qalrhlK~yaPLL~af~s~g~sE 338 (412)
T KOG2297|consen 259 KELQEQVSEEDPVKEVILYVKEEMKRNNLPETEVIGIVWSGIMSAVEWNKKEELVAEQALRHLKQYAPLLAAFCSQGQSE 338 (412)
T ss_pred HHHHHHhccCCCHHHHHHHHHHHHHhcCCCCceEEeeeHhhhhHHHhhchHHHHHHHHHHHHHHhhhHHHHHHhcCChHH
Confidence 456777788889999999999877655433 4678889999888876552 234455688999999999998888
Q ss_pred HHHHHHHHHHHhhCCCcchh---HHHHhhhccccChhhHHHhhc
Q 002930 577 LMLIEEVSLFWKNNTQNAAI---SIDRMMGYRLISNLAIVRWVF 617 (864)
Q Consensus 577 ~~il~~v~~~W~~~pQ~~~i---vvDkll~~~Iv~p~~Vv~W~F 617 (864)
..+|--|.+|=-.|-..+-. ||--|.+..+++-..|..|-=
T Consensus 339 L~Ll~KvQe~CYen~~fMKaFqkiV~lfYk~dVLsEe~IL~Wyk 382 (412)
T KOG2297|consen 339 LELLLKVQEYCYENIHFMKAFQKIVVLFYKADVLSEETILKWYK 382 (412)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence 98888888877666544321 344567778888888888864
No 21
>KOG1003 consensus Actin filament-coating protein tropomyosin [Cytoskeleton]
Probab=51.90 E-value=2.4e+02 Score=29.72 Aligned_cols=108 Identities=23% Similarity=0.283 Sum_probs=66.4
Q ss_pred HHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhccccCCCCCCCCChhhhhHhHHhHhhhhhhhhhHHHHHHHH
Q 002930 642 TYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKLSLVDGEPVLGGNPARLSRLKLHAEKAKNEEISAKESLEAK 721 (864)
Q Consensus 642 v~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 721 (864)
+.+|..+...++..+..++..|.+-+..|...-+.+.-++..++|. +++....++.+.+.-..+++++..+
T Consensus 51 ~enr~~kdEE~~e~~e~qLkEAk~iaE~adrK~eEVarkL~iiE~d---------LE~~eeraE~~Es~~~eLeEe~~~~ 121 (205)
T KOG1003|consen 51 IENRAQKLEEKMEAQEAQLKEAKHIAEKADRKYEEVARKLVIIEGE---------LERAEERAEAAESQSEELEEDLRIL 121 (205)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH---------HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4577777777888888887777777777766666666677776652 3333344444444444555555555
Q ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHhhhcCCCccCC
Q 002930 722 EALFARAVEENEALY--LSLYRNFSNVLMERLPDASRAG 758 (864)
Q Consensus 722 ~~~l~~a~~eqk~lf--l~~~~~Fi~~L~e~l~~~~~~~ 758 (864)
..-|.+...--..++ +..|..-+-.|++.|...++.+
T Consensus 122 ~~nlk~l~~~ee~~~q~~d~~e~~ik~ltdKLkEaE~rA 160 (205)
T KOG1003|consen 122 DSNLKSLSAKEEKLEQKEEKYEEELKELTDKLKEAETRA 160 (205)
T ss_pred HhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhhhhH
Confidence 444443322222222 3478888999999998776644
No 22
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=51.35 E-value=5e+02 Score=34.28 Aligned_cols=163 Identities=12% Similarity=0.145 Sum_probs=77.8
Q ss_pred HHHHHHHhcC-CCCHHHHHHHHHhhccCCCCchhHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhhCC------ChHH
Q 002930 503 SAELTNKVKG-RQTAREIIVWVEESVYPIHGLGVTIKVVVQTLLDIGSKSFTHLITVLERYGQVISKICP------DHDK 575 (864)
Q Consensus 503 a~~l~~~lk~-k~~~~ei~~~l~e~~~~~~g~~~~i~vfvq~ll~~GsKSfSH~~~~iery~~~lk~l~~------~~~~ 575 (864)
|.+.-..+++ ++.+++++..+.+...... ...-=-|-.+...+.|.+.+.........+++.+.+ .+..
T Consensus 1417 A~~~~~~l~~~~ae~eq~~~~v~ea~~~as----eA~~~Aq~~~~~a~as~~q~~~s~~el~~Li~~v~~Flt~~~adp~ 1492 (1758)
T KOG0994|consen 1417 AGDADTQLRSKLAEAEQTLSMVREAKLSAS----EAQQSAQRALEQANASRSQMEESNRELRNLIQQVRDFLTQPDADPD 1492 (1758)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHhhH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHH
Confidence 4444333333 3556777777765332111 111112444555677777777777776666666442 2233
Q ss_pred HH-HHHHHHHHHHhh-CCCcchhHHHHhhhccccChhhHHHhhcCccccccccccCchHHHHHHHHHHHHHhHHHHHHHH
Q 002930 576 QL-MLIEEVSLFWKN-NTQNAAISIDRMMGYRLISNLAIVRWVFSPENIDQFHASDRPWEVLRNAVSKTYNRICDLRKEI 653 (864)
Q Consensus 576 q~-~il~~v~~~W~~-~pQ~~~ivvDkll~~~Iv~p~~Vv~W~F~~~~~~~~~~~~~~WEil~~ti~kv~~rv~~~~~~l 653 (864)
++ .+-+.|...|.. .|+-+-.+.++.-. .|....=|.-|+.... +. .--=+.|..--++.+.+..++.+..
T Consensus 1493 si~~vA~~vL~l~lp~tpeqi~~L~~~I~e--~v~sL~nVd~IL~~T~-~d----i~ra~~L~s~A~~a~~~A~~v~~~a 1565 (1758)
T KOG0994|consen 1493 SIEEVAEEVLALELPLTPEQIQQLTGEIQE--RVASLPNVDAILSRTK-GD----IARAENLQSEAERARSRAEDVKGQA 1565 (1758)
T ss_pred HHHHHHHHHHhccCCCCHHHHHHHHHHHHH--HHHhcccHHHHHHhhh-hh----HHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 33 344556666654 44444444444311 1111111111111100 00 0122344444455666666666677
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHH
Q 002930 654 ISLKKGVTLAEEAAAKAKAELEA 676 (864)
Q Consensus 654 ~~~~~~~~~~~~~~~~~~~~~~~ 676 (864)
+..++.|+.|+.|..+|+..++.
T Consensus 1566 e~V~eaL~~Ad~Aq~~a~~ai~~ 1588 (1758)
T KOG0994|consen 1566 EDVVEALEEADVAQGEAQDAIQG 1588 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 77777777766666655544433
No 23
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=48.77 E-value=1.5e+02 Score=32.24 Aligned_cols=27 Identities=15% Similarity=0.281 Sum_probs=11.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHhhhhH
Q 002930 636 RNAVSKTYNRICDLRKEIISLKKGVTL 662 (864)
Q Consensus 636 ~~ti~kv~~rv~~~~~~l~~~~~~~~~ 662 (864)
..++..+-+.|.+...++++++++.+.
T Consensus 51 ~~e~e~le~qv~~~e~ei~~~r~r~~~ 77 (239)
T COG1579 51 EIELEDLENQVSQLESEIQEIRERIKR 77 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333334444444444444444444433
No 24
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=48.16 E-value=2.5e+02 Score=30.45 Aligned_cols=30 Identities=23% Similarity=0.395 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHhhhhH
Q 002930 633 EVLRNAVSKTYNRICDLRKEIISLKKGVTL 662 (864)
Q Consensus 633 Eil~~ti~kv~~rv~~~~~~l~~~~~~~~~ 662 (864)
..+..-+.....|+..++.+++.++++++.
T Consensus 59 ~~~~~~~~~~~~r~~~l~~~i~~~~~~i~~ 88 (302)
T PF10186_consen 59 QQLKREIEELRERLERLRERIERLRKRIEQ 88 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444444433
No 25
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=47.45 E-value=2.3e+02 Score=27.47 Aligned_cols=37 Identities=19% Similarity=0.295 Sum_probs=23.0
Q ss_pred HHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 002930 638 AVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAEL 674 (864)
Q Consensus 638 ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 674 (864)
.+.++...+++...++..+|.++...++.+..+..++
T Consensus 17 ~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Ei 53 (120)
T PF12325_consen 17 LVERLQSQLRRLEGELASLQEELARLEAERDELREEI 53 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666677777777776666555555555443
No 26
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=46.99 E-value=1.9e+02 Score=31.46 Aligned_cols=51 Identities=18% Similarity=0.234 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhc
Q 002930 631 PWEVLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKL 681 (864)
Q Consensus 631 ~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 681 (864)
..+-+.+=+...++++..+..++.+++.+....+....+.+...+.++.++
T Consensus 32 ~l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl 82 (239)
T COG1579 32 ALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKL 82 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555666777777777777777776666666666555555555554
No 27
>PRK09039 hypothetical protein; Validated
Probab=43.68 E-value=2.6e+02 Score=31.82 Aligned_cols=32 Identities=16% Similarity=0.306 Sum_probs=19.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHH
Q 002930 636 RNAVSKTYNRICDLRKEIISLKKGVTLAEEAA 667 (864)
Q Consensus 636 ~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~ 667 (864)
.......+..|..++.+++++|+++...+++.
T Consensus 129 k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L 160 (343)
T PRK09039 129 KQVSARALAQVELLNQQIAALRRQLAALEAAL 160 (343)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444566677777777777777765444433
No 28
>cd07600 BAR_Gvp36 The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Golgi vesicle protein of 36 kDa and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Proteomic analysis shows that Golgi vesicle protein of 36 kDa (Gvp36) may be involved in vesicular trafficking and nutritional adaptation. A Saccharomyces cerevisiae strain deficient in Gvp36 shows defects in growth, in actin cytoskeleton polarization, in endocytosis, in vacuolar biogenesis, and in the cell cycle. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=42.87 E-value=1.6e+02 Score=32.07 Aligned_cols=36 Identities=17% Similarity=0.272 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC
Q 002930 713 SAKESLEAKEALFARAVEENEALYLSLYRNFSNVLMERLPDA 754 (864)
Q Consensus 713 ~~~~~~e~~~~~l~~a~~eqk~lfl~~~~~Fi~~L~e~l~~~ 754 (864)
+.+..++.|+..++.+ + ++..++.||..=.+...+|
T Consensus 196 a~E~a~~~M~~il~~~--e----~i~~L~~fv~AQl~Yh~~~ 231 (242)
T cd07600 196 ATEEAVELMKEVLDNP--E----PLQLLKELVKAQLAYHKTA 231 (242)
T ss_pred hHHHHHHHHHHHHhhh--H----HHHHHHHHHHHHHHHHHHH
Confidence 3556677777776652 3 4566666777655554444
No 29
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=42.50 E-value=44 Score=29.72 Aligned_cols=53 Identities=13% Similarity=0.297 Sum_probs=43.7
Q ss_pred HHHHhhCCChHHHHHHHHHHHHHHhhCCCc---chhHHHHhhhccccChhhHHHhh
Q 002930 564 QVISKICPDHDKQLMLIEEVSLFWKNNTQN---AAISIDRMMGYRLISNLAIVRWV 616 (864)
Q Consensus 564 ~~lk~l~~~~~~q~~il~~v~~~W~~~pQ~---~~ivvDkll~~~Iv~p~~Vv~W~ 616 (864)
.+|+.+..+.+.|+.+|.++-.|-..++.. ...++..|.+..||+=.+|++|-
T Consensus 2 ~ll~~~~~~~~~q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~dileEe~il~W~ 57 (83)
T smart00515 2 PLLKFLAKDEEEQIDLLYAIEEFCVELEKLIKLLPKILKSLYDADILEEEAILKWY 57 (83)
T ss_pred hHHHHHHCChHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhhhccccHHHHHHHH
Confidence 468888888899999999999999765432 33466888999999999999997
No 30
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=42.16 E-value=1.5e+02 Score=37.69 Aligned_cols=77 Identities=22% Similarity=0.274 Sum_probs=47.2
Q ss_pred HHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhccccCCCCCCCCChhhhhHhHHhHhhhhhhhhhHHHHHH
Q 002930 640 SKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKLSLVDGEPVLGGNPARLSRLKLHAEKAKNEEISAKESLE 719 (864)
Q Consensus 640 ~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 719 (864)
.|+......++++|..+|.....|.++..+-..++.+..+.. + | ..-+.+.+.+.-.+++.++|
T Consensus 272 Skim~qqa~Lqrel~raR~e~keaqe~ke~~k~emad~ad~i-------------E-m--aTldKEmAEERaesLQ~eve 335 (1243)
T KOG0971|consen 272 SKIMEQQADLQRELKRARKEAKEAQEAKERYKEEMADTADAI-------------E-M--ATLDKEMAEERAESLQQEVE 335 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------H-H--HHhhHHHHHHHHHHHHHHHH
Confidence 467788888899999888877777666665555553322211 1 1 11112444444566777788
Q ss_pred HHHHHHHHHHHHH
Q 002930 720 AKEALFARAVEEN 732 (864)
Q Consensus 720 ~~~~~l~~a~~eq 732 (864)
..+|++++...+.
T Consensus 336 ~lkEr~deletdl 348 (1243)
T KOG0971|consen 336 ALKERVDELETDL 348 (1243)
T ss_pred HHHHHHHHHHHHH
Confidence 7777777665554
No 31
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=41.17 E-value=3.7e+02 Score=26.71 Aligned_cols=49 Identities=31% Similarity=0.281 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhc
Q 002930 633 EVLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKL 681 (864)
Q Consensus 633 Eil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 681 (864)
+-+..-+..+..+..+...+|.++.++....+....+....+..+...+
T Consensus 17 e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~l 65 (143)
T PF12718_consen 17 EELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELDKLEEQLKEAKEKL 65 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455566677777777777777777777777666666665555443
No 32
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=41.01 E-value=7.1e+02 Score=31.43 Aligned_cols=38 Identities=24% Similarity=0.334 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 002930 714 AKESLEAKEALFARAVEENEALYLSLYRNFSNVLMERLP 752 (864)
Q Consensus 714 ~~~~~e~~~~~l~~a~~eqk~lfl~~~~~Fi~~L~e~l~ 752 (864)
+++.-+++.+++++|.+.|+.|.-++ ++....+..+++
T Consensus 591 l~~~ae~LaeR~e~a~d~Qe~L~~R~-~~vl~~l~~~~P 628 (717)
T PF10168_consen 591 LRESAEKLAERYEEAKDKQEKLMKRV-DRVLQLLNSQLP 628 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhccCC
Confidence 66667788889999999999887662 334444444433
No 33
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=39.86 E-value=79 Score=29.24 Aligned_cols=81 Identities=19% Similarity=0.216 Sum_probs=54.9
Q ss_pred hhccccCcHHHHHHHHHHhC-CCCchHHHHHHHHHhcCChhHHHHHHHHHHHHHHHH--HhcCCchhHHHHHHHHhhccc
Q 002930 38 ELEHSSDDVPHYIINCAEQI-PHKIPLYGTLVGLLNLENEDFVKKVVETTQRKFQDA--LDSGNCDRIRILMRFLTVMMC 114 (864)
Q Consensus 38 el~~~~~~il~~l~~cv~e~-P~K~p~YAtLVgllN~kn~~~g~~ive~~~~~lq~~--L~~g~w~~~klllRFLa~Lvn 114 (864)
..+.+...++..++.|+.+. +.--+.|+.|+.-+..++.-....+...+..-++.. +....-.....+-+|+++++.
T Consensus 29 ~~~~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~ 108 (113)
T PF02847_consen 29 KLPSQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIA 108 (113)
T ss_dssp T-GGGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHH
Confidence 34566688999999999998 888899999999888877655555555554444332 122333456677888888866
Q ss_pred cccc
Q 002930 115 SKIL 118 (864)
Q Consensus 115 ~~Vi 118 (864)
.+++
T Consensus 109 ~~~l 112 (113)
T PF02847_consen 109 DGIL 112 (113)
T ss_dssp TTSS
T ss_pred cCCc
Confidence 5554
No 34
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=38.56 E-value=87 Score=29.07 Aligned_cols=80 Identities=21% Similarity=0.239 Sum_probs=55.3
Q ss_pred hccccCcHHHHHHHHHHhC-CCCchHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHh--cCCchhHHHHHHHHhhcccc
Q 002930 39 LEHSSDDVPHYIINCAEQI-PHKIPLYGTLVGLLNLENEDFVKKVVETTQRKFQDALD--SGNCDRIRILMRFLTVMMCS 115 (864)
Q Consensus 39 l~~~~~~il~~l~~cv~e~-P~K~p~YAtLVgllN~kn~~~g~~ive~~~~~lq~~L~--~g~w~~~klllRFLa~Lvn~ 115 (864)
.+++...++..++.|+.+. +.--+.|+.|+..+..++.-....+...+...++..=+ --.-+....+-+|++.++..
T Consensus 30 ~~~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~ 109 (113)
T smart00544 30 LPEQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISD 109 (113)
T ss_pred CCcchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHc
Confidence 3467788999999999997 57789999999988877766655555555554444211 11225666778888888766
Q ss_pred ccc
Q 002930 116 KIL 118 (864)
Q Consensus 116 ~Vi 118 (864)
+++
T Consensus 110 ~~l 112 (113)
T smart00544 110 GIL 112 (113)
T ss_pred CCC
Confidence 654
No 35
>COG4238 Murein lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=37.01 E-value=1.1e+02 Score=27.15 Aligned_cols=41 Identities=22% Similarity=0.371 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 002930 634 VLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAEL 674 (864)
Q Consensus 634 il~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 674 (864)
-+.+.+...+..|.++..++.+++.....|...+++|..++
T Consensus 29 qlss~vq~LnAkv~qLe~dv~a~~~~~qAAk~eaarAn~rl 69 (78)
T COG4238 29 QLSSDVQTLNAKVDQLENDVNAMRSDVQAAKDEAARANQRL 69 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHH
Confidence 35566677888888888888888887777776666666665
No 36
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=36.29 E-value=86 Score=28.63 Aligned_cols=25 Identities=12% Similarity=0.235 Sum_probs=14.8
Q ss_pred HHHHHHHhHHHHHHHHHHHHhhhhH
Q 002930 638 AVSKTYNRICDLRKEIISLKKGVTL 662 (864)
Q Consensus 638 ti~kv~~rv~~~~~~l~~~~~~~~~ 662 (864)
-+..++.++..+..++..++.++..
T Consensus 6 ~~~~l~~~l~~~~~q~~~l~~~~~~ 30 (106)
T PF01920_consen 6 KFQELNQQLQQLEQQIQQLERQLRE 30 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445666666666666666665543
No 37
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=33.22 E-value=77 Score=36.80 Aligned_cols=26 Identities=27% Similarity=0.312 Sum_probs=15.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH
Q 002930 712 ISAKESLEAKEALFARAVEENEALYL 737 (864)
Q Consensus 712 ~~~~~~~e~~~~~l~~a~~eqk~lfl 737 (864)
+.++++++.+|+.|+.|++||+++=.
T Consensus 255 q~aEqsl~dlQk~Lekar~e~rnvav 280 (575)
T KOG4403|consen 255 QRAEQSLEDLQKRLEKAREEQRNVAV 280 (575)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhchhh
Confidence 34566666666666666666666543
No 38
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=33.11 E-value=5e+02 Score=27.32 Aligned_cols=44 Identities=32% Similarity=0.385 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHH---HHHHHHH
Q 002930 635 LRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAK---AELEAAE 678 (864)
Q Consensus 635 l~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~---~~~~~~~ 678 (864)
|+.+|..+-..-.++..++.++++++.....+..+|+ .+++++.
T Consensus 27 L~~~ve~~ee~na~L~~e~~~L~~q~~s~Qqal~~aK~l~eEledLk 73 (193)
T PF14662_consen 27 LQRSVETAEEGNAQLAEEITDLRKQLKSLQQALQKAKALEEELEDLK 73 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6677777777777888889999988888777777763 4444443
No 39
>PRK09973 putative outer membrane lipoprotein; Provisional
Probab=33.10 E-value=1.7e+02 Score=26.84 Aligned_cols=40 Identities=23% Similarity=0.365 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 002930 635 LRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAEL 674 (864)
Q Consensus 635 l~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 674 (864)
|.+-+..++..+.++..++.++|.....|.+++++|-.++
T Consensus 29 Lss~V~~L~~kvdql~~dv~~a~aaa~aAk~EA~RAN~Ri 68 (85)
T PRK09973 29 LASNVQTLNAKIARLEQDMKALRPQIYAAKSEANRANTRL 68 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4445555555555666666666555544444444444443
No 40
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=32.50 E-value=4.3e+02 Score=24.84 Aligned_cols=37 Identities=14% Similarity=0.031 Sum_probs=17.4
Q ss_pred HhHHhHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 002930 699 RLKLHAEKAKNEEISAKESLEAKEALFARAVEENEAL 735 (864)
Q Consensus 699 ~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~l 735 (864)
.+++.-+.-+.....+++..+.++++++.+++..+.+
T Consensus 71 ~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~~ 107 (110)
T TIGR02338 71 ELKEKKETLELRVKTLQRQEERLREQLKELQEKIQEA 107 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333334445555555555555555544443
No 41
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=31.55 E-value=3.9e+02 Score=24.51 Aligned_cols=38 Identities=29% Similarity=0.226 Sum_probs=23.8
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Q 002930 709 NEEISAKESLEAKEALFARAVEENEA-LYLSLYRNFSNV 746 (864)
Q Consensus 709 ~~~~~~~~~~e~~~~~l~~a~~eqk~-lfl~~~~~Fi~~ 746 (864)
+|..++.+.++..|++|.....|... ..+.+.--|+-.
T Consensus 43 ~E~~~l~~~l~~~E~eL~~LrkENrK~~~ls~~l~~v~~ 81 (85)
T PF15188_consen 43 KELNELKEKLENNEKELKLLRKENRKSMLLSVALFFVCF 81 (85)
T ss_pred HHHHHHHHHhhccHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 34455777788888888888777554 444444344433
No 42
>PRK12472 hypothetical protein; Provisional
Probab=31.18 E-value=4e+02 Score=31.80 Aligned_cols=31 Identities=39% Similarity=0.474 Sum_probs=18.0
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHhhc
Q 002930 651 KEIISLKKGVTLAEEAAAKAKAELEAAESKL 681 (864)
Q Consensus 651 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 681 (864)
+++..+.+.+..+|++.+++.+++..++..+
T Consensus 218 ~~~~~~~~~l~~~e~~~~~a~~~l~~adk~l 248 (508)
T PRK12472 218 REAAPLKASLRKLERAKARADAELKRADKAL 248 (508)
T ss_pred HHhHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555555566666666666666665555443
No 43
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=30.80 E-value=1.5e+02 Score=36.75 Aligned_cols=70 Identities=16% Similarity=0.248 Sum_probs=54.3
Q ss_pred CcHHHHHHHHHHhCCCCchHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHhcCCchhHHHHHHHHhhccc
Q 002930 44 DDVPHYIINCAEQIPHKIPLYGTLVGLLNLENEDFVKKVVETTQRKFQDALDSGNCDRIRILMRFLTVMMC 114 (864)
Q Consensus 44 ~~il~~l~~cv~e~P~K~p~YAtLVgllN~kn~~~g~~ive~~~~~lq~~L~~g~w~~~klllRFLa~Lvn 114 (864)
-.|...++.|+.+--.--|+||+|..-+..-+..+..-+==-++..|+++ +.-.-.++..+.+|+++|+-
T Consensus 652 rEI~~VllhC~l~EK~yNpfYa~lA~KfCe~~~~~~~tfQF~~WD~f~el-e~ls~~ri~nLa~l~a~Li~ 721 (822)
T KOG2141|consen 652 REIARVLLHCCLNEKTYNPFYALLALKFCEFNKNLKKTFQFALWDRFKEL-EQLSLFRISNLAKLLASLIS 721 (822)
T ss_pred HHHHHHHHHHHhhhcccchHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh-hhcchhhHhHHHHHHHHHHH
Confidence 46899999999998889999999998888877666665555566666664 33455677888999999954
No 44
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=30.14 E-value=3.9e+02 Score=31.85 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=21.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHhhhh
Q 002930 636 RNAVSKTYNRICDLRKEIISLKKGVT 661 (864)
Q Consensus 636 ~~ti~kv~~rv~~~~~~l~~~~~~~~ 661 (864)
+.||+-+.+++++++++++++.++-+
T Consensus 58 ~DTlrTlva~~k~~r~~~~~l~~~N~ 83 (472)
T TIGR03752 58 ADTLRTLVAEVKELRKRLAKLISENE 83 (472)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788899999999999999987543
No 45
>PRK15396 murein lipoprotein; Provisional
Probab=29.73 E-value=2.1e+02 Score=25.72 Aligned_cols=40 Identities=23% Similarity=0.385 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 002930 635 LRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAEL 674 (864)
Q Consensus 635 l~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 674 (864)
|.+=+..++..+.++..++.++|.....|.+.+++|-.++
T Consensus 30 LssqV~~L~~kvdql~~dv~~~~~~~~~a~~eA~raN~Rl 69 (78)
T PRK15396 30 LSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRL 69 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555555555555555554444444444444333
No 46
>PF12061 DUF3542: Protein of unknown function (DUF3542); InterPro: IPR021929 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide. The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain []. Most proteins matching this entry are found associated with PF00931 from PFAM.
Probab=28.93 E-value=75 Score=35.76 Aligned_cols=113 Identities=17% Similarity=0.331 Sum_probs=69.5
Q ss_pred CchHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHhcCCch---------------hHHHHHHHHhhcccccccCcccHH
Q 002930 60 KIPLYGTLVGLLNLENEDFVKKVVETTQRKFQDALDSGNCD---------------RIRILMRFLTVMMCSKILQPGSLV 124 (864)
Q Consensus 60 K~p~YAtLVgllN~kn~~~g~~ive~~~~~lq~~L~~g~w~---------------~~klllRFLa~Lvn~~Vi~~~sl~ 124 (864)
|+|.-|.-| |..+|+|+-++++-++.++...++-++-. +=.-+|||+.|.+...++++.+-.
T Consensus 20 ~~~l~~nkv---~~~spkfVme~id~~V~Nlnvlvkindp~s~~Fv~gkeqIeqVlKELkLLRffV~fvsnk~iEpq~~~ 96 (402)
T PF12061_consen 20 KTSLAANKV---NIDSPKFVMEFIDVVVGNLNVLVKINDPCSWLFVPGKEQIEQVLKELKLLRFFVCFVSNKCIEPQYRH 96 (402)
T ss_pred CCccccccc---CCCCchhhhhhHHHHHhhhhhheecCCcchhhcCCchHHHHHHHHHHHHHHHheeeeeceeeccccch
Confidence 455544444 78899999999999999999988654431 122468999999999999988544
Q ss_pred -HHHHHHHHhhhhcccccCCCChhhhhhhHHHHHHHhhhhhccHHhhhhCHHHHHHHHHHHHHHHhhcccCCCC
Q 002930 125 -VVFETLLSSAATTVDEDKGNPSWQARADFYVTCILSCLPWGGAELIEQVPEEIERVMAGLEAYLSIRRHTSDT 197 (864)
Q Consensus 125 -~ll~~Ll~~a~~~~~~e~~~~~~q~r~D~~v~~vL~~LP~~G~eL~e~~~e~Le~ll~~ie~y~~~R~~~~~~ 197 (864)
.+|..-+-.| -+.+-++-.-+| |-.-..-.+.++.++++ .+++-+-++.++
T Consensus 97 ttFytHaL~~a-----------------sh~AMvvwL~lP--~n~nqdl~psEvs~LLs---df~~mkIk~i~P 148 (402)
T PF12061_consen 97 TTFYTHALIEA-----------------SHIAMVVWLHLP--GNGNQDLAPSEVSRLLS---DFMEMKIKSIQP 148 (402)
T ss_pred hhHHHHHHHHH-----------------HhhHheEEEecC--CCCCcccChHHHHHHHH---HHHhceeeccCC
Confidence 3333222211 122332334477 32222446788999865 455555444443
No 47
>PRK11637 AmiB activator; Provisional
Probab=28.78 E-value=3.9e+02 Score=31.16 Aligned_cols=21 Identities=10% Similarity=0.207 Sum_probs=10.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q 002930 713 SAKESLEAKEALFARAVEENE 733 (864)
Q Consensus 713 ~~~~~~e~~~~~l~~a~~eqk 733 (864)
.++.+++.+++.++.++.+.+
T Consensus 100 ~~~~ei~~l~~eI~~~q~~l~ 120 (428)
T PRK11637 100 QLNKQIDELNASIAKLEQQQA 120 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555444444433
No 48
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=28.76 E-value=3.6e+02 Score=27.75 Aligned_cols=16 Identities=38% Similarity=0.582 Sum_probs=6.3
Q ss_pred HhHHHHHHHHHHHHhh
Q 002930 644 NRICDLRKEIISLKKG 659 (864)
Q Consensus 644 ~rv~~~~~~l~~~~~~ 659 (864)
.|+..+-+++..++++
T Consensus 118 ~r~~~li~~l~~~~~~ 133 (192)
T PF05529_consen 118 RRVHSLIKELIKLEEK 133 (192)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333333344444443
No 49
>cd07617 BAR_Endophilin_B2 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain two endophilin-B isoforms. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle. Endophilin-B2, also called SH3GLB2 (SH3-domain GRB2-like endophilin B2), is a cytoplasmic protein that interacts with the apoptosis inducer Bax. It is overexpressed in prostate cancer metastasis and has been identified
Probab=28.39 E-value=4.8e+02 Score=28.02 Aligned_cols=47 Identities=21% Similarity=0.324 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhc
Q 002930 635 LRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKL 681 (864)
Q Consensus 635 l~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 681 (864)
|++++++-.+-+.+.|++|+..|=.++.......+|..+++.+++++
T Consensus 124 L~~~l~~dlk~i~k~RKkLe~rRLd~D~~K~r~~kae~elr~A~~kf 170 (220)
T cd07617 124 LRNFLEGDWKTISKERRLLQNRRLDLDACKARLKKAEHELRVAQTEF 170 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence 34444444444455555555544444333333334444555555554
No 50
>PF02020 W2: eIF4-gamma/eIF5/eIF2-epsilon; InterPro: IPR003307 This entry represents the W2 domain (two invariant tryptophans) and is a region of ~165 amino acids which is found in the C terminus of the following eIFs [, , , ]: Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon) Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included []. The W2 domain has a globular fold and is exclusively composed out of alpha-helices [, , ]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions. For example, the W2 domain of H. sapiens eIF5 binds eIF2-beta, eIF3 and eIF1 [], and therefore plays an important role in multifactor complex assembly. The entry covers the entire W2 domain.; GO: 0005488 binding; PDB: 3D3M_A 3L6A_A 1PAQ_A 2FUL_D 2IU1_A 1UG3_B 3JUI_A.
Probab=28.08 E-value=96 Score=27.71 Aligned_cols=45 Identities=18% Similarity=0.319 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHhhCCC---cchhHHHHhhhccccChhhHHHhhcC
Q 002930 574 DKQLMLIEEVSLFWKNNTQ---NAAISIDRMMGYRLISNLAIVRWVFS 618 (864)
Q Consensus 574 ~~q~~il~~v~~~W~~~pQ---~~~ivvDkll~~~Iv~p~~Vv~W~F~ 618 (864)
..|+.+|.++-.|=.+++. ....|+-.|.+..||+-.+|+.|-=+
T Consensus 2 ~~Q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~ 49 (84)
T PF02020_consen 2 DDQVDLLNALEEFCAENPNLMPLFPKILQQLYDEDILEEEAILEWYED 49 (84)
T ss_dssp HHHHHHHHHHHHHHHHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHc
Confidence 5788999999999988887 56678889999999999999999855
No 51
>PF07064 RIC1: RIC1; InterPro: IPR009771 This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [, , ].
Probab=27.74 E-value=1.8e+02 Score=31.78 Aligned_cols=68 Identities=26% Similarity=0.254 Sum_probs=42.7
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHhcCChhH--HHHHHHHHHHHHHHHHhcCCchhHHHHHHHHhhccccc
Q 002930 48 HYIINCAEQIPHKIPLYGTLVGLLNLENEDF--VKKVVETTQRKFQDALDSGNCDRIRILMRFLTVMMCSK 116 (864)
Q Consensus 48 ~~l~~cv~e~P~K~p~YAtLVgllN~kn~~~--g~~ive~~~~~lq~~L~~g~w~~~klllRFLa~Lvn~~ 116 (864)
+++-+|...--.| .++.-|+-+-|...... .++..+.+++-++.++++++|.-|+=++|||..|-.++
T Consensus 184 dLf~~cl~~~~l~-tAa~yLlVl~~~e~~~~~~~~~~~~~al~LL~~a~~~~~w~Lc~eL~RFL~~ld~~~ 253 (258)
T PF07064_consen 184 DLFEECLENGNLK-TAASYLLVLQNLEGSSVVKDEESRQCALRLLVMALESGDWDLCFELVRFLKALDPEG 253 (258)
T ss_pred HHHHHHHHcCcHH-HHHHHHHHHHhcCCcchhhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccc
Confidence 3444444443333 23333443434443332 34456777788888999999999999999999885544
No 52
>PF11570 E2R135: Coiled-coil receptor-binding R-domain of colicin E2; InterPro: IPR024566 Bacteriocins are protein antibiotics that kill bacteria closely related to the producing species. Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism. Most colicins are able to translocate the outer membrane by a two-receptor system, where one receptor is used for the initial binding and the second for translocation. The initial binding is to cell surface receptors such as the porins OmpF, FepA, BtuB, Cir and FhuA. The presence of specific periplasmic proteins, such as TolA, TolB, TolC, or TonB, are required for translocation across the membrane []. Colicins are composed of domains with distinct functional roles. In general they contain a central R (receptor) domain that mediates receptor binding, an N-terminal T (translocation) domain that mediates translocation of the protein from the outer membrane receptor to the colicin's target within the cell, and a C-terminal C (catalytic) domain that performs the catalytic cleavage []. This entry represents the central R domain found in colicin-E2 and other colicins.; PDB: 2YSU_B 1UJW_B 2B5U_C 1JCH_A.
Probab=27.64 E-value=4.2e+02 Score=26.14 Aligned_cols=41 Identities=22% Similarity=0.310 Sum_probs=20.4
Q ss_pred HHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhc
Q 002930 641 KTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKL 681 (864)
Q Consensus 641 kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 681 (864)
+...-+.++.++|..+...+..++.+....+.+++.++.++
T Consensus 12 ~a~aeL~~a~~~I~~~q~r~a~a~~~~~~r~seldqA~~~~ 52 (136)
T PF11570_consen 12 AARAELDQADEDIATLQERQASAEQALNGRRSELDQANKKV 52 (136)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 33344444444555555544555555555555555555444
No 53
>PF12777 MT: Microtubule-binding stalk of dynein motor; InterPro: IPR024743 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [].; PDB: 3VKH_A 3VKG_A 3ERR_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 2RR7_A.
Probab=27.16 E-value=2.1e+02 Score=32.46 Aligned_cols=85 Identities=25% Similarity=0.275 Sum_probs=48.9
Q ss_pred chHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhccccCCCCCCCCChhhhhHhHHhHhhhhh
Q 002930 630 RPWEVLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKLSLVDGEPVLGGNPARLSRLKLHAEKAKN 709 (864)
Q Consensus 630 ~~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 709 (864)
..|=.--....+|...|.-.+.++.++.+++..+++.....+.++...+..+ ..++..-+....
T Consensus 200 c~WV~A~~~Y~~v~~~V~P~~~~l~~a~~~l~~~~~~L~~~~~~l~~l~~~l----------------~~l~~~~~~~~~ 263 (344)
T PF12777_consen 200 CKWVRAMVKYYEVNKEVEPKRQKLEEAEAELEEAEEQLAEKQAELAELEEKL----------------AALQKEYEEAQK 263 (344)
T ss_dssp HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHH
Confidence 4454444445567777777888888887777766666665555554444332 233333333334
Q ss_pred hhhhHHHHHHHHHHHHHHHHH
Q 002930 710 EEISAKESLEAKEALFARAVE 730 (864)
Q Consensus 710 ~~~~~~~~~e~~~~~l~~a~~ 730 (864)
+...++++++..+.+|++|.+
T Consensus 264 e~~~l~~~~~~~~~kl~rA~~ 284 (344)
T PF12777_consen 264 EKQELEEEIEETERKLERAEK 284 (344)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhhccHHH
Confidence 445566666666666666543
No 54
>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....
Probab=26.32 E-value=5.3e+02 Score=27.58 Aligned_cols=32 Identities=16% Similarity=0.138 Sum_probs=16.8
Q ss_pred HhHhhhhhhhhhHHHHHHHHHHHHHHHHHHHH
Q 002930 702 LHAEKAKNEEISAKESLEAKEALFARAVEENE 733 (864)
Q Consensus 702 ~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk 733 (864)
.+++.+......++..++.+++.|......-+
T Consensus 190 ~Rae~aE~~v~~Le~~id~le~eL~~~k~~~~ 221 (237)
T PF00261_consen 190 NRAEFAERRVKKLEKEIDRLEDELEKEKEKYK 221 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444445566666666666655444433
No 55
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=26.30 E-value=7.2e+02 Score=27.52 Aligned_cols=29 Identities=17% Similarity=0.218 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHhhh
Q 002930 632 WEVLRNAVSKTYNRICDLRKEIISLKKGV 660 (864)
Q Consensus 632 WEil~~ti~kv~~rv~~~~~~l~~~~~~~ 660 (864)
=-+|+.||.-..-|+.+.+-+|.......
T Consensus 107 Ekvlk~aIq~i~~~~q~~~~~Lnnvasde 135 (338)
T KOG3647|consen 107 EKVLKSAIQAIQVRLQSSRAQLNNVASDE 135 (338)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence 34566777776677766666666655533
No 56
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=26.09 E-value=6.6e+02 Score=27.81 Aligned_cols=45 Identities=20% Similarity=0.231 Sum_probs=26.7
Q ss_pred hHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 002930 631 PWEVLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELE 675 (864)
Q Consensus 631 ~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 675 (864)
+=-.|..+|..+...+.+.++.+..+++.....++...+.+.|+|
T Consensus 163 iE~~l~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELE 207 (267)
T PF10234_consen 163 IEKALKEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELE 207 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334566777777777777777777766644444444444444443
No 57
>cd04378 RhoGAP_GMIP_PARG1 RhoGAP_GMIP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein) and PARG1 (PTPL1-associated RhoGAP1). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases ge
Probab=25.58 E-value=41 Score=35.17 Aligned_cols=35 Identities=11% Similarity=0.308 Sum_probs=29.8
Q ss_pred HHHHHhcCCCCchHHHHHHHHHHHhcCCCCcHHHHHH
Q 002930 375 IMDLCKALPGAFPAVVAGAVRALFDKIADLDMECRIR 411 (864)
Q Consensus 375 LiELCK~~P~~iapvlgrAir~ly~~l~~mD~e~~~R 411 (864)
|.++|+..|+.+|.++-+|+++++++ .|+.|-+.|
T Consensus 5 L~~~~~~~~~~vP~iv~~ci~~i~~~--gl~~eGIfR 39 (203)
T cd04378 5 FSQVPRDFPDEVPFIIKKCTSEIENR--ALGVQGIYR 39 (203)
T ss_pred hHHHHHHCCCCCChHHHHHHHHHHhc--CCCCcccee
Confidence 67899999999999999999999987 566666555
No 58
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=24.90 E-value=3.1e+02 Score=28.47 Aligned_cols=38 Identities=21% Similarity=0.164 Sum_probs=30.3
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002930 705 EKAKNEEISAKESLEAKEALFARAVEENEALYLSLYRN 742 (864)
Q Consensus 705 ~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~lfl~~~~~ 742 (864)
+.-.||-.+++-++..+++++..++.|.+.|.-+.+++
T Consensus 147 e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~Rwm~~ 184 (194)
T PF08614_consen 147 EILQDELQALQLQLNMLEEKLRKLEEENRELVERWMQR 184 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456777788888899999999999999988776553
No 59
>COG1422 Predicted membrane protein [Function unknown]
Probab=24.86 E-value=2.3e+02 Score=29.88 Aligned_cols=24 Identities=8% Similarity=0.187 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 002930 718 LEAKEALFARAVEENEALYLSLYR 741 (864)
Q Consensus 718 ~e~~~~~l~~a~~eqk~lfl~~~~ 741 (864)
+|++|++-.++.++|..+.-.-|+
T Consensus 100 lkkLq~~qmem~~~Q~elmk~qfk 123 (201)
T COG1422 100 LKKLQEKQMEMMDDQRELMKMQFK 123 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhh
Confidence 555555555667777777776665
No 60
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=24.40 E-value=1.9e+02 Score=30.51 Aligned_cols=26 Identities=12% Similarity=0.169 Sum_probs=17.3
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHH
Q 002930 709 NEEISAKESLEAKEALFARAVEENEA 734 (864)
Q Consensus 709 ~~~~~~~~~~e~~~~~l~~a~~eqk~ 734 (864)
+....++++|+.+|+.|..=+++...
T Consensus 167 ~Dl~~ie~QV~~Le~~L~~k~~eL~~ 192 (195)
T PF12761_consen 167 EDLDTIEEQVDGLESHLSSKKQELQQ 192 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455788888888887766555544
No 61
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=23.39 E-value=1.4e+03 Score=27.88 Aligned_cols=169 Identities=21% Similarity=0.166 Sum_probs=80.4
Q ss_pred hhhhHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHhhCCCcchhHHHHhhhccccChhhHHHhhcCccccccccccCc
Q 002930 551 SFTHLITVLERYGQVISKICPDHDKQLMLIEEVSLFWKNNTQNAAISIDRMMGYRLISNLAIVRWVFSPENIDQFHASDR 630 (864)
Q Consensus 551 SfSH~~~~iery~~~lk~l~~~~~~q~~il~~v~~~W~~~pQ~~~ivvDkll~~~Iv~p~~Vv~W~F~~~~~~~~~~~~~ 630 (864)
=+.+++.=|..|-+..+.|...-..=.+=|+.+-..|..+..-+-.+.+ ..|-+...++.
T Consensus 43 El~~LNDRLA~YIekVR~LEaqN~~L~~di~~lr~~~~~~ts~ik~~ye----~El~~ar~~l~---------------- 102 (546)
T KOG0977|consen 43 ELQELNDRLAVYIEKVRFLEAQNRKLEHDINLLRGVVGRETSGIKAKYE----AELATARKLLD---------------- 102 (546)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcchhHHhh----hhHHHHHHHHH----------------
Confidence 3557888888898888888754321112234444555555444322221 11111111111
Q ss_pred hHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhccccCCCCCCCCChhhhhHhHHhHhhhhhh
Q 002930 631 PWEVLRNAVSKTYNRICDLRKEIISLKKGVTLAEEAAAKAKAELEAAESKLSLVDGEPVLGGNPARLSRLKLHAEKAKNE 710 (864)
Q Consensus 631 ~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 710 (864)
-...-..|+-.-+.+++.++.++|+++..++..+..++.+.+.....+.. -.+...-++..-..-.++
T Consensus 103 ---e~~~~ra~~e~ei~kl~~e~~elr~~~~~~~k~~~~~re~~~~~~~~l~~---------leAe~~~~krr~~~le~e 170 (546)
T KOG0977|consen 103 ---ETARERAKLEIEITKLREELKELRKKLEKAEKERRGAREKLDDYLSRLSE---------LEAEINTLKRRIKALEDE 170 (546)
T ss_pred ---HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhhhhh---------hhhHHHHHHHHHHHHHHH
Confidence 11112234556677777788888887777665555555555433333211 111111222222222233
Q ss_pred hhhHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhhhc
Q 002930 711 EISAKESLEAKEALFARAVE--ENEALYLSLYRNFSNVLMERL 751 (864)
Q Consensus 711 ~~~~~~~~e~~~~~l~~a~~--eqk~lfl~~~~~Fi~~L~e~l 751 (864)
...+..+..++.+.|+.+.. +|+-+.-+=+|.=+..|.+.|
T Consensus 171 ~~~Lk~en~rl~~~l~~~r~~ld~Etllr~d~~n~~q~Lleel 213 (546)
T KOG0977|consen 171 LKRLKAENSRLREELARARKQLDDETLLRVDLQNRVQTLLEEL 213 (546)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 34455555566555555543 444444444444444444443
No 62
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=23.26 E-value=4.7e+02 Score=29.87 Aligned_cols=16 Identities=19% Similarity=0.335 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHhhcc
Q 002930 177 IERVMAGLEAYLSIRR 192 (864)
Q Consensus 177 Le~ll~~ie~y~~~R~ 192 (864)
...+++-|..|...|+
T Consensus 22 ~~~~l~lls~~~sL~P 37 (365)
T KOG2391|consen 22 RQDLLNLLSSFKSLRP 37 (365)
T ss_pred HHHHHHHHHhccccCc
Confidence 3444555555555544
No 63
>PF10455 BAR_2: Bin/amphiphysin/Rvs domain for vesicular trafficking; InterPro: IPR018859 Endocytosis and intracellular transport involve several mechanistic steps: (1) for the internalisation of cargo molecules, the membrane needs to bend to form a vesicular structure, which requires membrane curvature and a rearrangement of the cytoskeleton; (2) following its formation, the vesicle has to be pinched off the membrane; (3) the cargo has to be subsequently transported through the cell and the vesicle must fuse with the correct cellular compartment. Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs)-domain, which is required for their in vivo function and their ability to tubulate membranes []. The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases. This entry identifies several fungal BAR domain proteins, such as Gvp36, that are not found by IPR004148 from INTERPRO [].
Probab=23.02 E-value=4.8e+02 Score=29.18 Aligned_cols=25 Identities=8% Similarity=0.173 Sum_probs=17.4
Q ss_pred HHhccchhhhHHHHH-HHHHHHHHhh
Q 002930 545 LDIGSKSFTHLITVL-ERYGQVISKI 569 (864)
Q Consensus 545 l~~GsKSfSH~~~~i-ery~~~lk~l 569 (864)
--.--|||+|.++-. ......|..+
T Consensus 115 ~~~~PKTl~~ALSraa~~ss~~l~~l 140 (289)
T PF10455_consen 115 SPSQPKTLYHALSRAALTSSEILEEL 140 (289)
T ss_pred ccCCCccHHHHHHHHHHHhHHHHHhc
Confidence 334578999988755 4566677777
No 64
>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=22.82 E-value=1.3e+03 Score=28.29 Aligned_cols=34 Identities=9% Similarity=-0.101 Sum_probs=25.8
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 002930 806 IGEKEQWCLSTLGYVKAFSRQYASEIWPHMEKLDA 840 (864)
Q Consensus 806 ~~~~~~W~~~~~g~~~~~~~~~~~~i~~~~~~l~~ 840 (864)
.+-+..|+.....++.++.++.|+..-+-+ ||+.
T Consensus 413 ~d~k~~V~~~l~el~~ei~~~~~~~~~~~~-tLq~ 446 (581)
T KOG0995|consen 413 VDLKSYVKPLLKELLDEISEELHEAENELE-TLQE 446 (581)
T ss_pred ccchhHhHHHHHHHHHHHHHHHHHHHHHHH-HHHH
Confidence 345788998999999999999998766544 4443
No 65
>PF08146 BP28CT: BP28CT (NUC211) domain; InterPro: IPR012954 This C-terminal domain is found in BAP28-like nucleolar proteins []. The bap28 mutation leads to abnormalities in the brain, starting at midsomitogenesis stages. Mutant zebrafish embryos display excessive apoptosis, especially in the central nervous system (CNS) that results in death. The mutation affects a gene that encodes a large protein with high similarity to the uncharacterised human protein BAP28 and lower similarity to yeast Utp10. Utp10 is a component of a nucleolar U3 small nucleolar RNA-containing RNP complex that is required for transcription of ribosomal DNA and for processing of 18 S rRNA. Zebrafish Bap28 is also required for rRNA transcription and processing, with a major effect on 18S rRNA maturation. Bap28 is therefore required for cell survival in the CNS through its role in rRNA synthesis and processing [].
Probab=22.65 E-value=92 Score=31.28 Aligned_cols=79 Identities=18% Similarity=0.156 Sum_probs=51.7
Q ss_pred CchhhHHHHHHHHhhcCCCCCCcchhHHHHHHHHHhcCCCCchH------HHHHHHHHHHhcCCCCcHHHHHHHHHHHHh
Q 002930 345 RYEYLMAETIFSQLLLLPQPPFKPIYYTLVIMDLCKALPGAFPA------VVAGAVRALFDKIADLDMECRIRFILWFSH 418 (864)
Q Consensus 345 k~E~~iVEtIfs~lf~LP~p~~~~vYY~slLiELCK~~P~~iap------vlgrAir~ly~~l~~mD~e~~~Rf~dWFS~ 418 (864)
++|..++++.....++|....++|+|+..+=-..-.+....-++ +|-+-+.-|++++.++=+--...+++=...
T Consensus 36 ~vE~~v~~~~~~lV~KLnE~~FRPlF~~l~dWA~~~l~~~~~~~~~~R~itfy~l~~~l~e~LKslf~~Y~~~ll~~~~~ 115 (153)
T PF08146_consen 36 EVESSVISAFVSLVLKLNEATFRPLFLKLVDWATSGLPKSDSSGSRARLITFYRLLNALAEKLKSLFTPYFSYLLDNAVD 115 (153)
T ss_pred HHHHHHHHHHHHHHHHcccchhHhHHHHHHHHHcccCCcccCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999875433322222222222 344455556666665555555556666666
Q ss_pred hhccc
Q 002930 419 HLSNF 423 (864)
Q Consensus 419 HLSNF 423 (864)
+|.++
T Consensus 116 ~L~~~ 120 (153)
T PF08146_consen 116 LLKQF 120 (153)
T ss_pred HHHHh
Confidence 66665
No 66
>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=21.95 E-value=9.4e+02 Score=25.27 Aligned_cols=48 Identities=25% Similarity=0.324 Sum_probs=33.2
Q ss_pred CchHHHHHHHHHHHHHhHHHH-------HHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 002930 629 DRPWEVLRNAVSKTYNRICDL-------RKEIISLKKGVTLAEEAAAKAKAELEA 676 (864)
Q Consensus 629 ~~~WEil~~ti~kv~~rv~~~-------~~~l~~~~~~~~~~~~~~~~~~~~~~~ 676 (864)
.+.|+.+...+.|...+..++ ..++..+++.+..++++...|+.+-+.
T Consensus 114 ~~~~~~~~~~L~k~~~~~~Kl~~~~~s~~~K~~~~~~ei~~~e~~~~~a~~~~e~ 168 (216)
T cd07627 114 WQYWQSAESELSKKKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASELKKEFEE 168 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999888666665 346667777766666666666655533
No 67
>PRK10698 phage shock protein PspA; Provisional
Probab=21.89 E-value=8.5e+02 Score=25.99 Aligned_cols=35 Identities=6% Similarity=0.123 Sum_probs=28.4
Q ss_pred chHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhHHH
Q 002930 630 RPWEVLRNAVSKTYNRICDLRKEIISLKKGVTLAE 664 (864)
Q Consensus 630 ~~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~ 664 (864)
--.+-...++.++...+.+++.++.++|.+....-
T Consensus 106 ~~~~~~~~~~~~L~~~l~~L~~ki~eak~k~~~L~ 140 (222)
T PRK10698 106 HEVTLVDETLARMKKEIGELENKLSETRARQQALM 140 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677888899999999999999999988765543
No 68
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=21.40 E-value=7.5e+02 Score=27.55 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=16.6
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHH
Q 002930 706 KAKNEEISAKESLEAKEALFARA 728 (864)
Q Consensus 706 ~~~~~~~~~~~~~e~~~~~l~~a 728 (864)
++.-|..++++-||.|..-|...
T Consensus 121 EARkEIkQLkQvieTmrssL~ek 143 (305)
T PF15290_consen 121 EARKEIKQLKQVIETMRSSLAEK 143 (305)
T ss_pred HHHHHHHHHHHHHHHHHhhhchh
Confidence 34456677888899888777655
No 69
>cd07592 BAR_Endophilin_A The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins are accessory proteins, localized at synapses, which interact with the endocytic proteins, dynamin and synaptojanin. They are essential for synaptic vesicle formation from the plasma membrane. They interact with voltage-gated calcium channels, thus linking vesicle endocytosis to calcium regulation. They also play roles in virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms. Endophilin-A proteins are enriched in the bra
Probab=21.32 E-value=8.2e+02 Score=26.25 Aligned_cols=25 Identities=16% Similarity=0.373 Sum_probs=15.4
Q ss_pred HhccchhhhHHHHHHHHHHHHHhhCCC
Q 002930 546 DIGSKSFTHLITVLERYGQVISKICPD 572 (864)
Q Consensus 546 ~~GsKSfSH~~~~iery~~~lk~l~~~ 572 (864)
.+|..| ++=.+|.+|.+....|+..
T Consensus 79 elg~~S--~~G~aL~~~g~a~~kIa~~ 103 (223)
T cd07592 79 ELGEDS--NFGQALVEVGEALKQLAEV 103 (223)
T ss_pred hcCCCC--hHHHHHHHHHHHHHHHHHH
Confidence 344444 4556777777777777654
No 70
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=21.11 E-value=9.9e+02 Score=25.22 Aligned_cols=33 Identities=12% Similarity=0.224 Sum_probs=26.3
Q ss_pred chHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhH
Q 002930 630 RPWEVLRNAVSKTYNRICDLRKEIISLKKGVTL 662 (864)
Q Consensus 630 ~~WEil~~ti~kv~~rv~~~~~~l~~~~~~~~~ 662 (864)
--++-+..++.++..++.+++.++.++|.+...
T Consensus 106 ~~~~~~~~~v~~l~~~l~~L~~ki~~~k~k~~~ 138 (219)
T TIGR02977 106 RELAAVEETLAKLQEDIAKLQAKLAEARARQKA 138 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778888888888888888888888886553
No 71
>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins.
Probab=20.85 E-value=2.1e+03 Score=28.98 Aligned_cols=35 Identities=9% Similarity=0.119 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhHhhccCCCChhhHHH
Q 002930 820 VKAFSRQYASEIWPHMEKLDAEVLSEDTHPLFRRA 854 (864)
Q Consensus 820 ~~~~~~~~~~~i~~~~~~l~~~~ft~~~~~~~~~~ 854 (864)
..+--..+..++..+-....+.|=..|+||..+..
T Consensus 741 i~~~~~~~~~~~~~le~~~~~eL~~~GvD~~~I~~ 775 (1201)
T PF12128_consen 741 IAAAKQEAKEQLKELEQQYNQELAGKGVDPERIQQ 775 (1201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 34444556666667777777777678999976543
No 72
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=20.84 E-value=7e+02 Score=28.60 Aligned_cols=13 Identities=31% Similarity=0.225 Sum_probs=4.9
Q ss_pred HHHHHHHHHHHHh
Q 002930 646 ICDLRKEIISLKK 658 (864)
Q Consensus 646 v~~~~~~l~~~~~ 658 (864)
+.++..+...+.+
T Consensus 139 ~~~l~~~~~~L~~ 151 (342)
T PF06632_consen 139 NSRLQAENEHLQK 151 (342)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 73
>KOG3595 consensus Dyneins, heavy chain [Cytoskeleton]
Probab=20.49 E-value=2.2e+03 Score=29.46 Aligned_cols=69 Identities=9% Similarity=0.134 Sum_probs=36.7
Q ss_pred chhHHHHHHHHHHHhcc----chhhhHHHHHHHHHHHHHhhCC--ChHHHHHHHHHHHHHHhhCCCcchhHHHHh
Q 002930 533 LGVTIKVVVQTLLDIGS----KSFTHLITVLERYGQVISKICP--DHDKQLMLIEEVSLFWKNNTQNAAISIDRM 601 (864)
Q Consensus 533 ~~~~i~vfvq~ll~~Gs----KSfSH~~~~iery~~~lk~l~~--~~~~q~~il~~v~~~W~~~pQ~~~ivvDkl 601 (864)
++..+.+.++|+|.+=. .|.=++...+-+-.-.+..+.. .+..-..+.+-+..+|..+|-.....+++.
T Consensus 831 PP~~Vk~~meavciLlg~~~~~~w~~~~~~~~~~~~fl~~l~~~~~~~i~~~~~k~i~~~~~~~p~f~~~~v~~~ 905 (1395)
T KOG3595|consen 831 PPHAVKLVMEAVCILLGRLSSTDWKNISKLLLSDDFFLIILREFDKDEIPEEIMKLIKKFYFQNPDFVPEKVNRA 905 (1395)
T ss_pred CcHHHHHHHHHHHHHhccccCCChHHHHHHhhcccHHHHHhhcCccccChHHHHHHHHHhhcCCccCCHHHHHhh
Confidence 35788889998887654 3333333333222222222221 222334566666777777777766555554
No 74
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Probab=20.26 E-value=1e+03 Score=25.78 Aligned_cols=34 Identities=15% Similarity=0.201 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002930 714 AKESLEAKEALFARAVEENEALYLSLYRNFSNVL 747 (864)
Q Consensus 714 ~~~~~e~~~~~l~~a~~eqk~lfl~~~~~Fi~~L 747 (864)
..+..+++-.++..+.+.-+..+-.++.+|+.+|
T Consensus 125 ~r~e~~~ml~evK~~~E~y~k~~k~~~~gi~aml 158 (230)
T PF03904_consen 125 VREENKSMLQEVKQSHEKYQKRQKSMYKGIGAML 158 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 4555566655566666666666666666665554
Done!